WO2017070256A2 - Méthode de criblage d'inhibiteurs de ras - Google Patents

Méthode de criblage d'inhibiteurs de ras Download PDF

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WO2017070256A2
WO2017070256A2 PCT/US2016/057774 US2016057774W WO2017070256A2 WO 2017070256 A2 WO2017070256 A2 WO 2017070256A2 US 2016057774 W US2016057774 W US 2016057774W WO 2017070256 A2 WO2017070256 A2 WO 2017070256A2
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seq
mutant
ras
mutant ras
amino acid
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PCT/US2016/057774
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WO2017070256A3 (fr
WO2017070256A8 (fr
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Matthew P. Patricelli
Ulf Peters
Liangsheng Li
Pingda Ren
Yi Liu
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Araxes Pharma Llc
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Priority to JP2018519718A priority Critical patent/JP2018533939A/ja
Priority to EP16858163.5A priority patent/EP3364977A4/fr
Priority to US15/342,100 priority patent/US9810690B2/en
Publication of WO2017070256A2 publication Critical patent/WO2017070256A2/fr
Publication of WO2017070256A3 publication Critical patent/WO2017070256A3/fr
Publication of WO2017070256A8 publication Critical patent/WO2017070256A8/fr
Priority to US15/713,297 priority patent/US20180246102A1/en

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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/573—Immunoassay; Biospecific binding assay; Materials therefor for enzymes or isoenzymes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y306/00—Hydrolases acting on acid anhydrides (3.6)
    • C12Y306/05—Hydrolases acting on acid anhydrides (3.6) acting on GTP; involved in cellular and subcellular movement (3.6.5)
    • C12Y306/05002—Small monomeric GTPase (3.6.5.2)
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/536—Immunoassay; Biospecific binding assay; Materials therefor with immune complex formed in liquid phase
    • G01N33/542—Immunoassay; Biospecific binding assay; Materials therefor with immune complex formed in liquid phase with steric inhibition or signal modification, e.g. fluorescent quenching
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/90—Enzymes; Proenzymes
    • G01N2333/91—Transferases (2.)
    • G01N2333/912—Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2500/00—Screening for compounds of potential therapeutic value
    • G01N2500/04—Screening involving studying the effect of compounds C directly on molecule A (e.g. C are potential ligands for a receptor A, or potential substrates for an enzyme A)
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2500/00—Screening for compounds of potential therapeutic value
    • G01N2500/20—Screening for compounds of potential therapeutic value cell-free systems

Definitions

  • Ras proteins such as KRAS, HRAS, and NRAS are common oncogenic mutations present in human malignancies, including but not limited to colorectal cancer, lung cancer, thyroid cancer, and ovarian cancer.
  • Ras in particular KRAS
  • KRAS has been well known as a primary cancer causing protein for more than 30 years
  • no effective treatments for Ras mutant tumors are currently available.
  • the pharmaceutical industry has invested tremendous resources into the development of Ras and Ras pathway inhibitors with limited success to date.
  • drugs have been approved targeting kinases involved in signal transduction downstream of Ras (e.g., RAF and MEK kinases). However, even in these cases, their effectiveness in Ras mutant tumors remains to be demonstrated.
  • the present disclosure provides assay strategies that enable robust and high throughput interrogation of Ras binding, such as in the Switch II binding pocket, and provides other advantages as well.
  • This pocket has been shown to inhibit Ras function both biochemically and in cells (see e.g., Ostrem, J.M.; Peters, U.; Sos, M.L.; Wells, J.A.; Shokat, K.M. Nature 2013, 503, 548-551, which is entirely incorporated herein by reference).
  • the assays are amenable to the predominant oncogenic mutations in any isoform of Ras (e.g., KRAS, HRAS, and RAS).
  • the methods described herein provide a direct measure of binding to a specific site on Ras (e.g., the Switch II pocket) that is targetable by small molecules and has been shown to affect Ras function.
  • the method also presents advantages over in vitro functional assays (e.g., nucleotide exchange, effector binding) in its ease of implementation, its throughput, and the fact that it can specifically identify direct Ras binders with a very low possibility of showing hits from compounds with indirect effects (e.g., binding to Ras effectors or binding to protein complex interfaces).
  • the present disclosure provides methods, compositions, reaction mixtures, mutant Ras proteins, kits, substrates, and systems for selecting a Ras antagonist, with high specificity and sensitivity. Selection of Ras antagonists according to the disclosure is significantly higher in throughput and efficiency.
  • the present disclosure provides a method of selecting a Ras antagonist.
  • the method comprises: (a) combining in a reaction mixture a mutant Ras, a competition probe, and a test compound; and (b) detecting a decrease in binding between the mutant Ras and the competition probe as compared to binding of the competition probe to the mutant Ras in the absence of the test compound; wherein: (i) the mutant Ras comprises a cysteine mutation; (ii) the competition probe is capable of binding and covalently modifying the mutant Ras; and (iii) the decrease in binding between the mutant Ras and the competition probe is indicative of Ras antagonist activity of the test compound.
  • the competition probe competes for binding in the Switch II pocket of the mutant Ras.
  • the competition probe is capable of covalently modifying the mutant Ras by reacting with the cysteine residue of the cysteine mutation.
  • the competition probe is selected from a compound in Table 2 or Table 3.
  • the competition probe is selected from the group consisting of CP-001, CP-002, CP-003, CP-004, CP-005, CP-006, CP-007, CP-008, CP-009, CP-010, CP-011, CP- 012, CP-013, CP-014, CP-015, CP-016, CP-017, CP-018, CP-019, CP-020, and any combination thereof.
  • the cysteine mutation is not at position 12 or 13 relative to SEQ ID NO: 1 when optimally aligned. In some embodiments, the cysteine mutation is at position 12 or 13 relative to SEQ ID NO: 1 when optimally aligned. In some embodiments, the cysteine mutation is at position 12 or 13 relative to SEQ ID NO: 1 when optimally aligned, and the mutant Ras is selected from the group consisting of MRAS, ERAS, RRAS2, RALA, RALB, RIT1, and any combination thereof. In some embodiments, the cysteine mutation is at a non-conserved amino acid position.
  • the cysteine mutation is a mutation relative to SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, or SEQ ID NO: 26 when optimally aligned.
  • the cysteine mutation is at position 62 relative to SEQ ID NO: 1 when optimally aligned (e.g., E62C in KRAS, HRAS, or NRAS; E72C in MRAS; AIOOC in ERAS; E73C in RRAS2, RALA, or RALB; A80C in RIT1), position 92 relative to SEQ ID NO: 1 when optimally aligned (e.g., D92C in KRAS, HRAS, or NRAS; H102C in MRAS; Q130C in ERAS; E103C in RRAS2; A103C in RALA or RALB; El IOC in RIT1), or position 95 relative to SEQ ID NO: 1 when optimally aligned (e.g., H95C in KRAS; Q95C in HRAS; L95C in NRAS; R105C in MRAS; Q133C in ERAS; K106C in RRAS2; D106C in RALA; E106C
  • the mutant Ras is a mutant Ras subfamily protein. In some embodiments, the Ras is a Ras subfamily protein. In some embodiments, the mutant Ras is selected from the group consisting of mutant KRAS, mutant HRAS, mutant NRAS, mutant MRAS, mutant ERAS, mutant RRAS2, mutant RALA, mutant RALB, mutant RIT1, and any combination thereof. In some embodiments, the Ras is selected from the group consisting of KRAS, HRAS, NRAS, MRAS, ERAS, RRAS2, RALA, RALB, RIT1, and any combination thereof. In some embodiments, the mutant Ras comprises one or more additional mutations.
  • the mutant Ras is selected from the group consisting of SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, and any combination thereof.
  • the test compound interacts with Ras via a chemical bond selected from the group consisting of a hydrogen bond, van der Waals interaction, ionic bond, covalent bond, hydrophobic interaction, and any combination thereof.
  • the test compound interacts with the Switch II binding pocket of Ras.
  • the test compound binds to a GDP -bound Ras protein with a K d of at most 100 ⁇ , thereby antagonizing Ras activity.
  • antagonizing Ras activity comprises modulating GTPase activity, nucleotide exchange, effector protein binding, effector protein activation, guanine exchange factor (GEF) binding, GEF-facilitated nucleotide exchange, phosphate release, nucleotide release, nucleotide binding, Ras subcellular localization, Ras post-translational processing, or Ras post-translational modification.
  • the test compound inhibits the binding or release of GDP or GTP to a Ras protein.
  • the test compound is selected from the group consisting of CP-023 (l-(4-(6- chloro-2-(3-(dimethylamino)propoxy)-8-fluoro-7-(3-hydroxynaphthalen-l-yl)quinazolin-4- yl)piperazin-l-yl)ethanone), CP-024 (4-(6-chloro-2-(3-(dimethylamino)propoxy)-8-fluoro-7- (3-hydroxynaphthalen-l-yl)quinazolin-4-yl)piperazine-l-carbaldehyde), and any combination thereof.
  • detecting the decrease in binding comprises measuring the fraction of Ras covalently modified by the competition probe as determined by mass spectrometry.
  • the disclosure provides a method of producing a Ras antagonist.
  • the method comprises selecting the Ras antagonist according to any of the methods described herein, and synthesizing the compound.
  • the disclosure provides a pharmaceutical composition comprising a Ras antagonist or pharmaceutically acceptable salt thereof selected according to any of the methods described herein.
  • the disclosure provides a reaction mixture comprising a mutant Ras, a competition probe that is capable of binding the mutant Ras, and a test compound.
  • the mutant Ras comprises a cysteine mutation;
  • the competition probe is capable of covalently modifying the mutant Ras at the cysteine mutation; and the test compound inhibits covalent modification of the mutant Ras by the competition probe.
  • the competition probe competes for binding in the Switch II pocket of the mutant Ras.
  • the cysteine mutation is not at position 12 or 13 relative to SEQ ID NO: 1 when optimally aligned. In some embodiments, the cysteine mutation is at position 12 or 13 relative to SEQ ID NO: 1 when optimally aligned.
  • the cysteine mutation is at position 12 or 13 relative to SEQ ID NO: 1 when optimally aligned, and the mutant Ras is selected from mutant MRAS, mutant ERAS, mutant RRAS2, mutant RALA, mutant RALB, mutant RITl, and any combination thereof. In some embodiments, the cysteine mutation is at a non-conserved amino acid position.
  • the cysteine mutation is at position 62 relative to SEQ ID NO: 1 when optimally aligned (e.g., E62C in KRAS, HRAS, or NRAS; E72C in MRAS; AIOOC in ERAS; E73C in RRAS2, RALA, or RALB; A80C in RIT1), position 92 relative to SEQ ID NO: 1 when optimally aligned (e.g., D92C in KRAS, HRAS, or NRAS; H102C in MRAS; Q130C in ERAS; E103C in RRAS2; A103C in RALA or RALB; El IOC in RIT1), or position 95 relative to SEQ ID NO: 1 when optimally aligned (e.g., H95C in KRAS; Q95C in HRAS; L95C in NRAS; R105C in MRAS; Q133C in ERAS; K106C in RRAS2; D106C in RALA; E106C
  • the mutant Ras is selected from the group consisting of mutant KRAS, mutant HRAS, mutant NRAS, mutant MRAS, mutant ERAS, mutant RRAS2, mutant RALA, mutant RALB, mutant RIT1, and any combination thereof.
  • the mutant Ras comprises one or more additional mutations.
  • the test compound interacts with Ras via a chemical bond selected from the group consisting of a hydrogen bond, van der Waals interaction, ionic bond, covalent bond, hydrophobic interaction, and any combination thereof.
  • the test compound interacts with the Switch II binding pocket of Ras.
  • the test compound is selected from the group consisting of CP-023 (l-(4-(6-chloro-2-(3- (dimethylamino)propoxy)-8-fluoro-7-(3-hydroxynaphthalen-l-yl)quinazolin-4-yl)piperazin- l-yl)ethanone), CP-024 (4-(6-chloro-2-(3-(dimethylamino)propoxy)-8-fluoro-7-(3- hydroxynaphthalen-l-yl)quinazolin-4-yl)piperazine-l-carbaldehyde), and any combination thereof.
  • the disclosure provides a mutant Ras comprising at least one substituted amino acid.
  • the substituted amino acid is a reactive amino acid that permits covalent conjugation between the mutant Ras and a competition probe exhibiting the ability to react with the reactive amino acid; and (b) the substituted amino acid is not a cysteine or an aspartic acid at position 12 or 13 relative to SEQ ID NO: 1 when optimally aligned.
  • the reactive amino acid is cysteine, lysine, tyrosine, aspartic acid, glutamic acid, or a non-natural amino acid.
  • the reactive amino acid is cysteine.
  • the competition probe is capable of binding the mutant Ras.
  • the competition probe competes for binding in the Switch II pocket of the mutant Ras.
  • the substituted amino acid is at a non-conserved position in Ras. In some embodiments, the substituted amino acid is at position 62, 92, or 95 relative to SEQ ID NO: 1 when optimally aligned. In some
  • the substituted amino acid is a cysteine at position 62 relative to SEQ ID NO: 1 when optimally aligned (e.g., E62C in KRAS, HRAS, or NRAS; E72C in MRAS; AIOOC in ERAS; E73C in RRAS2, RALA, or RALB; A80C in RITl), a cysteine at position 92 relative to SEQ ID NO: 1 when optimally aligned (e.g., D92C in KRAS, HRAS, or NRAS; H102C in MRAS; Q130C in ERAS; E103C in RRAS2; A103C in RALA or RALB; El IOC in RITl), or a cysteine at position 95 relative to SEQ ID NO: 1 when optimally aligned (e.g., H95C in KRAS; Q95C in HRAS; L95C in NRAS; R105C in MRAS; Q133C in ERAS;
  • the mutant Ras is selected from the group consisting of mutant KRAS, mutant HRAS, mutant NRAS, mutant MRAS, mutant ERAS, mutant RRAS2, mutant RALA, mutant RALB, mutant RITl, and any combination thereof.
  • the mutant Ras is selected from the group consisting of SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, and any combination thereof.
  • the mutant Ras comprises one or more additional mutations, such as a mutation at a position selected from positions 12, 13, 14, 18, 19, 22, 59, 60, 61, 63, 117, 146, and any combination thereof relative to SEQ ID NO: 1 when optimally aligned.
  • the one or more additional mutations comprises a mutation at a position selected from position 12, 13, 18, 61, 117, 146, and any combination thereof relative to SEQ ID NO: 1 when optimally aligned.
  • the one or more additional mutations comprise a mutation at a position selected from positions 12 and 13 relative to SEQ ID NO: 1 when optimally aligned.
  • the one or more additional mutations comprises a cysteine at position 12, an aspartic acid at position 12, a cysteine at position 13, an aspartic acid at position 13, or any combination thereof relative to SEQ ID NO: 1 when optimally aligned.
  • the disclosure provides a mutant Ras comprising a substituted amino acid, wherein: (a) the substituted amino acid is a reactive amino acid that permits covalent conjugation between the mutant Ras and a competition probe exhibiting the ability to react with the reactive amino acid; (b) the substituted amino acid is a cysteine or an aspartic acid at position 12 or 13 relative to SEQ ID NO: 1 when optimally aligned; and (c) the mutant Ras is selected from the group consisting of mutant MRAS, mutant ERAS, mutant RRAS2, mutant RALA, mutant RALB, mutant RITl, and any combination thereof.
  • the reactive amino acid is cysteine.
  • the competition probe is capable of binding the mutant Ras.
  • the competition probe competes for binding in the Switch II pocket of the mutant Ras.
  • the mutant Ras is selected from the group consisting of RALA, RALB, and any combination thereof.
  • the mutant Ras comprises one or more additional mutations.
  • the one or more additional mutations comprises a mutation at a position selected from position 12, 13, 14, 18, 19, 22, 59, 60, 61, 63, 117, 146, and any combination thereof relative to SEQ ID NO: 1 when optimally aligned, such as from position 12, 13, 18, 61, 117, 146, and any combination thereof relative to SEQ ID NO: 1 when optimally aligned.
  • the mutant Ras is Kras, having mutations of G12D and D92C, or mutations of G12D and H95C.
  • the disclosure provides a polynucleotide encoding any mutant Ras described herein.
  • the polynucleotide comprises DNA or RNA.
  • the disclosure provides an expression vector comprising any of the polynucleotides described herein.
  • the disclosure provides a host cell comprising any of the
  • the disclosure provides a host cell comprising any of the expression vectors described herein.
  • the disclosure provides a kit.
  • the kit comprises (a) a mutant Ras having a cysteine mutation at a position other than position 12 or 13 relative to SEQ ID NO: 1 when optimally aligned; and (b) instructions for using the mutant Ras in a competition reaction between a competition probe and a test compound.
  • the kit further comprises the competition probe. In some embodiments, the kit further comprises one or more test compounds.
  • the disclosure provides a substrate having attached thereto a complex comprising a mutant Ras and a competition probe.
  • the mutant Ras comprises a substituted amino acid that is a reactive amino acid that permits covalent conjugation between the mutant Ras and the competition probe;
  • the substituted amino acid is not a cysteine or an aspartic acid at position 12 or 13 relative to SEQ ID NO: 1 when optimally aligned; and
  • the competition probe is covalently bound to the mutant Ras at the reactive amino acid.
  • the substrate is in a form selected from the group consisting of beads, microparticles, nanoparticles, nanocrystals, fibers, microfibers, nanofibers, nanowires, nanotubes, mats, planar sheets, planar wafers or slides, multi-well plates, optical slides, flow cells, channels, and any combination thereof.
  • the substrate comprises a material selected from the group consisting of glass, quartz, fused silica, silicon, metal, polymers, plastics, ceramics, composite materials, and any combination thereof.
  • the disclosure provides a system for selecting a Ras antagonist.
  • the system comprises: (a) a computer configured to receive a user request to perform a competition reaction; (b) a reaction module that prepares the competition reaction, the competition reaction comprising a mutant Ras, a competition probe that is capable of binding the mutant Ras, and a test compound; (c) a detection module that detects a decrease in binding between the mutant Ras and the competition probe as compared to binding of the mutant Ras in the absence of the test compound; and (d) a report generator that sends a report to a recipient, wherein the report contains results from the detection module; wherein (i) the mutant Ras comprises a cysteine mutation that is not at position 12 or 13 relative to SEQ ID NO: 1 when optimally aligned; (ii) the competition probe is capable of covalently modifying the mutant Ras at the cysteine mutation; and (iii) the test compound inhibits covalent modification of the mutant Ras by the competition probe.
  • the report comprises: (a) a computer configured to receive
  • Fig. 1 illustrates an example of a competitive binding assay, in accordance with an embodiment.
  • a mutant Ras comprises a substituted amino acid (Z) (e.g., E62C, D92C, H95C relative to SEQ ID NO: 1 when optimally aligned) and optionally one or more additional mutations (e.g., an oncogenic mutation such as G12X or Q61X relative to SEQ ID NO: 1 when optimally aligned).
  • Z substituted amino acid
  • additional mutations e.g., an oncogenic mutation such as G12X or Q61X relative to SEQ ID NO: 1 when optimally aligned
  • a competition probe is capable of binding the mutant Ras, for example, in the Switch II pocket (110).
  • the competition probe may contain a reactive moiety (Y) (e.g., an electrophilic group) and an optional affinity and/or detection tag (120).
  • Y reactive moiety
  • 120 optional affinity and/or detection tag
  • the competition probe may be capable of covalently modifying the mutant Ras, for example, by reacting through its reactive moiety with the substituted amino acid to form a covalent bond (130).
  • a test compound (TEST) is a potential Switch II pocket binder. The extent of reaction (e.g., binding or covalent modification of the mutant Ras) in the competition reaction in the presence of a test compound is compared to the extent of reaction in the control reaction in the absence of a test compound.
  • Fig. 2 shows that exemplary substituted amino acid sites, including but not limited to position 62 (220), position 95 (240), and position 92 (260), are near the Switch II pocket (230) of Ras (210).
  • a mutant Ras may optionally comprise an additional mutation at position 12 (250). Positions are relative to SEQ ID NO: 1 when optimally aligned.
  • Fig. 3 shows that exemplary sites for substituted amino acid introduction (highlighted in black), including but not limited to position 62, position 95, and position 92, are not highly conserved in Ras family GTPases. Positions are relative to SEQ ID NO: 1 when optimally aligned.
  • Fig. 4 shows that KRAS, HRAS, NRAS, RALA, and RALB have high sequence conservation. Boxed positions indicate residues in the Switch II pocket. Position 12 in KRAS, HRAS, and NRAS is equivalent to position 23 in RALA and RALB.
  • Fig. 5 shows that RAL proteins have a preformed Switch II pocket. Apo Ral A GDP structure is shown. RCSB protein data bank structure 1U90.
  • Fig. 6 shows inhibition of competition probe depletion by D92C K-Ras in the presence of a test compound selected from CP-023 (l-(4-(6-chloro-2-(3- (dimethylamino)propoxy)-8-fluoro-7-(3-hydroxynaphthalen-l-yl)quinazolin-4-yl)piperazin- l-yl)ethanone), and CP-024 (4-(6-chloro-2-(3-(dimethylamino)propoxy)-8-fluoro-7-(3- hydroxynaphthalen-l-yl)quinazolin-4-yl)piperazine-l-carbaldehyde).
  • CP-008 100 nM
  • test compound were incubated for 6 h. Depletion of CP-008 was determined by mass spectrometry against a non-reactive internal standard compound.
  • Ras refers to a protein in the Ras superfamily of small GTPases, such as in the Ras subfamily.
  • the Ras superfamily includes, but is not limited to, the Ras subfamily, Rho subfamily, Rab subfamily, Rap subfamily, Arf subfamily, Ran subfamily, Rheb subfamily, RGK subfamily, Rit subfamily, Miro subfamily, and Unclassified subfamily.
  • a Ras protein is selected from the group consisting of KRAS, HRAS, RAS, MRAS, ERAS, RRAS2, RALA, RALB, RIT1, and any combination thereof, such as from KRAS, HRAS, NRAS, RALA, RALB, and any combination thereof.
  • Non-limiting examples of a Ras subfamily protein include DIRAS1; DIRAS2; DIRAS3; ERAS; GEM; HRAS;
  • Rho subfamily protein examples include RHOA; RHOB; RHOBTBl; RHOBTB2; RHOBTB3; RHOC; RHOD; RHOF; RHOG; RHOH; RHOJ; RHOQ; RHOU; RHOV; RND1; RND2; RND3; RAC1; RAC2; RAC3; and CDC42.
  • Non-limiting examples of a Rab subfamily protein include RABIA; RAB IB; RAB2; RAB 3 A; RAB3B; RAB3C; RAB3D; RAB4A; RAB4B; RAB5A; RAB5B; RAB5C; RAB 6 A; RAB6B; RAB6C; RAB 7 A; RAB7B; RAB7L1;
  • RABl lB RAB 12; RAB13; RAB14; RAB15; RAB 17; RAB 18; RAB 19; RAB20; RAB21; RAB22A; RAB23; RAB24; RAB25; RAB26; RAB27A; RAB27B; RAB28; RAB2B;
  • Rap subfamily protein examples include RAP1A; RAP1B;
  • Non-limiting examples of an Arf subfamily protein include ARFl; ARF3; ARF4; ARF5; ARF6; ARLl; ARL2; ARL3; ARL4; ARL5; ARL5C; ARL6; ARL7; ARL8; ARL9; ARLl OA; ARLIOB; ARLIOC; ARLl l; ARL13A; ARL13B; ARL14; ARL15; ARL16; ARL17; TRIM23, ARL4D; ARFRPl; and ARL13B.
  • Non-limiting examples of a Ran subfamily protein include RAN.
  • Non-limiting examples of a Rheb subfamily protein include RHEB and RHEBLl .
  • Non-limiting examples of a RGK subfamily protein include RRAD; GEM; REM; and REM2.
  • Non-limiting examples of a Rit subfamily protein include RIT1 and RIT2.
  • Non-limiting examples of a Miro subfamily protein include RHOTl and RHOT2.
  • Non-limiting examples of an Unclassified subfamily protein include ARHGAP5; DNAJC27; GRLF1; and RASEF.
  • Non-limiting examples of a RAL protein include RALA and RALB.
  • a Ras may be further modified, such as by conjugation with a detectable label.
  • a Ras is a full-length or truncated polypeptide.
  • a Ras may be a truncated polypeptide comprising residues 1-169 or residues 11-183 (e.g., residues 11-183 of RALA or RALB).
  • Wild Ras and “Ras mutant” refer to a Ras protein with one or more amino acid mutations, such as with respect to a common reference sequence such as a wild-type (WT) sequence.
  • a mutant Ras is selected from a mutant KRAS, mutant HRAS, mutant NRAS, mutant MRAS, mutant ERAS, mutant RRAS2, mutant RALA, mutant RALB, mutant RIT1, and any combination thereof, such as from a mutant KRAS, mutant HRAS, mutant NRAS, mutant RALA, mutant RALB, and any combination thereof.
  • a mutation may be an introduced mutation, a naturally occurring mutation, or a non-naturally occurring mutation.
  • a mutation may be a substitution (e.g., a substituted amino acid), insertion (e.g., addition of one or more amino acids), or deletion (e.g., removal of one or more amino acids).
  • two or more mutations may be consecutive, non-consecutive, or a combination thereof.
  • a mutation may be present at any position of Ras.
  • a mutation may be present at position 12, 13, 62, 92, 95, or any combination thereof of Ras relative to SEQ ID NO: 1 when optimally aligned.
  • a mutant Ras may comprise about or at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, or more than 50 mutations. In some embodiments, a mutant Ras may comprise up to about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, or 50 mutations.
  • the mutant Ras is about or up to about 500, 400, 300, 250, 240, 233, 230, 220, 219, 210, 208, 206, 204, 200, 195, 190, 189, 188, 187, 186, 185, 180, 175, 174, 173, 172, 171, 170, 169, 168, 167, 166, 165, 160, 155, 150, 125, 100, 90, 80, 70, 60, 50, or fewer than 50 amino acids in length.
  • an amino acid of a mutation is a proteinogenic, natural, standard, non-standard, non- canonical, essential, non-essential, or non-natural amino acid.
  • an amino acid of a mutation has a positively charged side chain, a negatively charged side chain, a polar uncharged side chain, a non-polar side chain, a hydrophobic side chain, a hydrophilic side chain, an aliphatic side chain, an aromatic side chain, a cyclic side chain, an acyclic side chain, a basic side chain, or an acidic side chain.
  • a mutation comprises a reactive moiety.
  • a substituted amino acid comprises a reactive moiety.
  • a mutant Ras may be further modified, such as by conjugation with a detectable label.
  • a mutant Ras is a full-length or truncated polypeptide.
  • a mutant Ras may be a truncated polypeptide comprising residues 1-169 or residues 1 1-183 (e.g., residues 1 1 -183 of a mutant RALA or mutant RALB).
  • Switch II pocket and "switch II binding pocket” refer to a binding pocket formed under the "Switch ⁇ " loop of Ras (see Fig. 2 and Fig. 5).
  • the Switch II pocket is located between the central ⁇ -sheet of Ras and the a2- and a3 -helices.
  • the Switch II binding pocket is located about or at least about 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 1 10, 120, 130, 140, 150, 160, 170, 180, 190, or 200 nm from position 12, position 60, position 99, or any combination thereof.
  • the Switch II binding pocket is located up to about 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 1 10, 120, 130, 140, 150, 160, 170, 180, 190, or 200 nm from position 12, position 60, position 99, or any combination thereof.
  • a competition probe refers to compound capable of binding a mutant Ras.
  • a competition probe is capable of binding Ras.
  • a competition probe may be capable of covalently modifying a mutant Ras, for example, through a reactive moiety.
  • a competition probe may be capable of binding in the Switch II pocket of a mutant Ras.
  • a competition probe may be a Ras antagonist.
  • a competition probe comprises a reactive moiety (e.g., an electrophilic group, a nucleophilic group).
  • Test compound refers to a compound screened for the capability of binding a mutant Ras.
  • a test compound may be capable of binding Ras and/or a mutant Ras.
  • a test compound may be capable of binding in the Switch II pocket of Ras and/or a mutant Ras.
  • a test compound may be a Ras antagonist.
  • Fig. 3 shows optimally aligned amino acid sequences for 51- amino acid segments of KRAS, HRAS, NRAS, MRAS, RRAS2, RALA, and RIT1 and a 48- amino acid segment of ERAS.
  • position 62 of KRAS, position 62 of HRAS, position 62 of NRAS, position 72 of MRAS, position 100 of ERAS, position 73 of RRAS2, position 73 of RALA, and position 80 of RIT1 correspond to position 62 of SEQ ID NO: 1 when optimally aligned.
  • Fig. 3 shows optimally aligned amino acid sequences for 51- amino acid segments of KRAS, HRAS, NRAS, MRAS, RRAS2, RALA, and RIT1 and a 48- amino acid segment of ERAS.
  • position 62 of KRAS, position 62 of HRAS, position 62 of NRAS, position 73 of RALA, and position 73 of RALB correspond to position 62 of SEQ ID NO: 1 when optimally aligned.
  • position 12 of KRAS, position 12 of HRAS, position 12 of NRAS, position 23 of RALA, and position 23 of RALB correspond to position 12 of SEQ ID NO: 1 when optimally aligned.
  • Amino acid mutations are relative to SEQ ID NO: 1 when optimally aligned.
  • G12C of KRAS, G12C of HRAS, G12C of NRAS, G23C of RALA, and G23C of RALB correspond to G12C of SEQ ID NO: 1 when optimally aligned.
  • E62C of KRAS, E62C of HRAS, E62C of NRAS, E73C of RALA, and E73C of RALB correspond to E62C of SEQ ID NO: 1 when optimally aligned.
  • D92C of KRAS, D92C of HRAS, D92C of NRAS, A103C of RALA, and A103C of RALB correspond to D92C of SEQ ID NO: 1 when optimally aligned.
  • H95C of KRAS, Q95C of HRAS, L95C of NRAS, D106C of RALA, and E106C of RALB correspond to H95C of SEQ ID NO: 1 when optimally aligned.
  • Reactive moiety refers to any moiety that facilitates attachment by a chemical reaction (e.g., covalent bond formation) or a binding interaction.
  • a reactive moiety is a nucleophilic group such as a sulfur-containing group (e.g., thiol, thiolate, cysteine), nitrogen-containing group (e.g., amine, azide, alkoxyamine, hydrazine), carbon- containing group (e.g., enol, enolate, tyrosine, aniline, alkene, alkyne), phosphorus- containing group (e.g., phosphine compounds such as a triaryl phosphine), or oxygen- containing group (e.g., alcohol, alkoxide).
  • a sulfur-containing group e.g., thiol, thiolate, cysteine
  • nitrogen-containing group e.g., amine, azide, alkoxyamine, hydrazine
  • a reactive moiety is an electrophilic group such as an alkene, alkyne, aldehyde, ketone, N-hydroxysuccinimide ester, sulfo-N-hydroxysuccinimide ester, imidoester, sulfonyl chloride, carbodiimide, acyl azide, fluorobenzene, carbonate, fluorophenyl ester, maleimide, iodoacetamide, 2-thiopyridone, 3- carboxy-4-nitrothiophenol, epoxide, isothiocyanate, diazonium compound, isocyanate, anhydride, conjugated double bond, ⁇ , ⁇ -unsaturated carbonyl, acrylamide, vinyl
  • a reactive moiety is biotin, streptavidin, or avidin.
  • Electrophile and “electrophilic group” refer to any moiety capable of reacting with a nucleophile (e.g., a moiety having a lone pair of electrons, a negative charge, a partial negative charge and/or an excess of electrons, for example a -SH group). Electrophiles typically are electron poor or comprise atoms which are electron poor. In certain embodiments, an electrophile contains a positive charge or partial positive charge, has a resonance structure which contains a positive charge or partial positive charge, or is a moiety in which derealization or polarization of electrons results in one or more atoms which contain a positive charge or partial positive charge.
  • the electrophile comprises conjugated double bonds, for example an ⁇ , ⁇ -unsaturated carbonyl, acrylamide, vinyl sulfonamide, or ⁇ , ⁇ -unsaturated thiocarbonyl compound.
  • the electrophile is capable of covalent and/or irreversible binding to a cysteine thiol group.
  • the electrophile is capable of forming a covalent bond with a mutant Ras protein, such as at position 62, 92, or 95 of a mutant Ras.
  • antagonists are used interchangeably, and they refer to a compound having the ability to antagonize a biological function (e.g., activity, expression, binding, protein-protein interaction) of a target protein (e.g., Ras, mutant Ras, KRAS, HRAS, NRAS). Accordingly, the terms “antagonist” and “inhibitor” are defined in the context of the biological role of the target protein. While preferred antagonists herein specifically interact with (e.g., bind to) the target, compounds that inhibit a biological activity of the target protein by interacting with other members of the signal transduction pathway of which the target protein is a member are also specifically included within this definition. A preferred biological activity inhibited by an antagonist is associated with the development, growth, or spread of a tumor.
  • agonist refers to a compound having the ability to initiate or enhance a biological function of a target protein, such as by triggering the activity or expression of the target protein. Accordingly, the term “agonist” is defined in the context of the biological role of the target polypeptide. While preferred agonists herein specifically interact with (e.g., bind to) the target, compounds that initiate or enhance a biological activity of the target polypeptide by interacting with other members of the signal transduction pathway of which the target polypeptide is a member are also specifically included within this definition.
  • Signal transduction is a process during which stimulatory or inhibitory signals are transmitted into and within a cell to elicit an intracellular response.
  • a modulator of a signal transduction pathway refers to a compound which modulates the activity of one or more cellular proteins mapped to the same specific signal transduction pathway.
  • a modulator may augment (agonist) or suppress (antagonist) the activity of a signaling molecule.
  • polynucleotide refers to a polymeric form of nucleotides of any length, including deoxyribonucleotides or ribonucleotides, or analogs thereof.
  • Polynucleotides may have any three dimensional structure, and may perform any function, known or unknown.
  • the following are non-limiting examples of polynucleotides: coding or non-coding regions of a gene or gene fragment, loci (locus) defined from linkage analysis, exons, introns, messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), short interfering RNA (siRNA), short-hairpin RNA (shRNA), micro-RNA (miRNA), ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, expression vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers.
  • a polynucleotide may comprise one or more modified nucleotides, such as methylated nucleotides and nucleotide analogs. If present, modifications to the nucleotide structure may be imparted before or after assembly of the polymer. The sequence of nucleotides may be interrupted by non-nucleotide components. A polynucleotide may be further modified after polymerization, such as by conjugation with a detectable label.
  • “Expression” refers to the process by which a polynucleotide is transcribed from a DNA template (such as into mRNA or other RNA transcript) and/or the process by which a transcribed mRNA is subsequently translated into peptides, polypeptides, or proteins.
  • Transcripts and encoded polypeptides may be collectively referred to as "gene product.” If the polynucleotide is derived from genomic DNA, expression may include splicing of the mRNA in a eukaryotic cell.
  • polypeptide polypeptide
  • peptide protein
  • the terms “polypeptide”, “peptide”, and “protein” are used interchangeably herein to refer to polymers of amino acids of any length.
  • the polymer may be linear or branched, may comprise modified amino acids, and may be interrupted by non amino acids.
  • the terms also encompass an amino acid polymer that has been modified, for example, by disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation, such as conjugation with a detectable label.
  • amino acid includes natural and/or unnatural or synthetic amino acids, including glycine, cysteine, and both the D or L optical isomers, and amino acid analogs and peptidomimetics.
  • an amino acid is a proteinogenic, natural, standard, non-standard, non-canonical, essential, non-essential, or non-natural amino acid.
  • an amino acid has a positively charged side chain, a negatively charged side chain, a polar uncharged side chain, a non-polar side chain, a hydrophobic side chain, a hydrophilic side chain, an aliphatic side chain, an aromatic side chain, a cyclic side chain, an acyclic side chain, a basic side chain, or an acidic side chain.
  • an amino acid has a nucleophilic or electrophilic side chain.
  • conjugate and “conjugated to” are intended to indicate the formation of a composite molecule by the covalent attachment of one or more proteins or small molecules to any of the articles of the invention described herein.
  • Covalent attachment means that the two elements described are either directly covalently joined to each other (e.g., via a carbon- carbon bond), or are indirectly covalently joined to one another via an intervening chemical structure, such as a bridge, spacer, linker, linkage group, or any combination thereof.
  • bridge refers to a molecular fragment that connects two distinct chemical elements (e.g., an inhibitor and a fluorophore).
  • spacer or “linker” are used
  • linkage group is intended to mean a chemical functional group capable of covalently joining two or more chemical elements (e.g., a phosphoryl or sulfonyl group).
  • Control refers to an alternative subject or sample used in an experiment for comparison purpose.
  • a “control reaction” refers to a reaction, to which a competition reaction is compared.
  • a control reaction comprises the mutant Ras and competition probe but not the test compound of a competition reaction to which it is compared.
  • the control reaction may consist of the same contents by identity and quantity as the competition reaction but without the test compound.
  • determining can be used interchangeably herein to refer to any form of measurement, and include determining if an element is present or not (for example, detection). These terms can include both quantitative and/or qualitative determinations. Assessing may be relative or absolute. "Detecting the presence of can include determining the amount of something present and/or determining whether it is present or absent.
  • Sequence comparisons such as for the purpose of assessing identities, mutations, or where one or more positions of a test sequence fall relative to one or more specified positions of a reference sequence (e.g., SEQ ID NO: 1), may be performed by any suitable alignment algorithm, including but not limited to the Needleman-Wunsch algorithm (see e.g., the EMBOSS Needle aligner available at www.ebi.ac.uk/Tools/psa/emboss_needle/, optionally with default settings), the BLAST algorithm (see e.g., the BLAST alignment tool available at blast.ncbi.nlm.nih.gov/Blast.cgi, optionally with default settings), and the Smith-Waterman algorithm (see e.g., the EMBOSS Water aligner available at
  • Optimal alignment may be assessed using any suitable parameters of a chosen algorithm, including default parameters.
  • sequence identity refers to an exact nucleotide-to-nucleotide or amino acid-to-amino acid correspondence of two polynucleotides or polypeptide sequences, respectively.
  • techniques for determining sequence identity include determining the nucleotide sequence of a polynucleotide and/or determining the amino acid sequence encoded thereby, and comparing these sequences to a second nucleotide or amino acid sequence.
  • Two or more sequences can be compared by determining their "percent identity.”
  • the percent identity to a reference sequence e.g., nucleic acid or amino acid sequences
  • a reference sequence e.g., nucleic acid or amino acid sequences
  • Percent identity may also be determined, for example, by comparing sequence information using the advanced BLAST computer program, including version 2.2.9, available from the National Institutes of Health.
  • the BLAST program is based on the alignment method of Karlin and Altschul, Proc. Natl. Acad. Sci.
  • the BLAST program defines identity as the number of identical aligned symbols (i.e., nucleotides or amino acids), divided by the total number of symbols in the shorter of the two sequences.
  • the program may be used to determine percent identity over the entire length of the sequences being compared. Default parameters are provided to optimize searches with short query sequences, for example, with the blastp program.
  • the program also allows use of an SEG filter to mask-off segments of the query sequences as determined by the SEG program of Wootton and Federhen, Computers and Chemistry 17: 149-163 (1993). Ranges of desired degrees of sequence identity are
  • an exact match indicates 100%> identity over the length of the reference sequence.
  • effective amount or “therapeutically effective amount” refers to that amount of a compound described herein that is sufficient to affect the intended application, including but not limited to disease treatment, as defined below.
  • the therapeutically effective amount may vary depending upon the intended treatment application (in vivo), or the subject and disease condition being treated, e.g., the weight and age of the subject, the severity of the disease condition, the manner of administration and the like, which can readily be determined by one of ordinary skill in the art.
  • the term also applies to a dose that will induce a particular response in target cells, e.g., reduction of platelet adhesion and/or cell migration.
  • the specific dose will vary depending on the particular compounds chosen, the dosing regimen to be followed, whether it is administered in combination with other compounds, timing of administration, the tissue to which it is administered, and the physical delivery system in which it is carried.
  • treatment refers to an approach for obtaining beneficial or desired results with respect to a disease, disorder, or medical condition including but not limited to a therapeutic benefit and/or a prophylactic benefit.
  • therapeutic benefit is meant eradication or amelioration of the underlying disorder being treated.
  • a therapeutic benefit is achieved with the eradication or amelioration of one or more of the physiological symptoms associated with the underlying disorder such that an improvement is observed in the subject, notwithstanding that the subject may still be afflicted with the underlying disorder.
  • the compositions are administered to a subject at risk of developing a particular disease, or to a subject reporting one or more of the physiological symptoms of a disease, even though a diagnosis of this disease may not have been made.
  • a prophylactic effect includes delaying or eliminating the appearance of a disease or condition, delaying or eliminating the onset of symptoms of a disease or condition, slowing, halting, or reversing the progression of a disease or condition, or any combination thereof.
  • co-administration encompass administration of two or more agents to an animal, including humans, so that both agents and/or their metabolites are present in the subject at the same time.
  • Co-administration includes simultaneous administration in separate compositions, administration at different times in separate compositions, or administration in a composition in which both agents are present.
  • “Pharmaceutically acceptable salt” includes both pharmaceutically acceptable acid addition salts and pharmaceutically acceptable base addition salts.
  • “Pharmaceutically acceptable acid addition salt” refers to those salts which retain the biological effectiveness and properties of the free bases, which are not biologically or otherwise desirable, and which are formed with inorganic acids such as, but are not limited to, hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid and the like, or organic acids such as, but not limited to, acetic acid, 2,2-dichloroacetic acid, adipic acid, alginic acid, ascorbic acid, aspartic acid, benzenesulfonic acid, benzoic acid, 4- acetamidobenzoic acid, camphoric acid, camphor- 10-sulfonic acid, capric acid, caproic acid, caprylic acid, carbonic acid, cinnamic acid, citric acid, cyclamic acid, dodecyl sulfuric acid, ethane-l,2-disulfonic acid, ethanesulfonic acid, 2-hydroxyethanesul
  • “Pharmaceutically acceptable base addition salt” refers to those salts which retain the biological effectiveness and properties of the free acids, which are not biologically or otherwise desirable. These salts are prepared from addition of an inorganic base or an organic base to the free acid. Salts derived from inorganic bases include, but are not limited to, the sodium, potassium, lithium, ammonium, calcium, magnesium, iron, zinc, copper, manganese, aluminum salts and the like. Preferred inorganic salts are the ammonium, sodium, potassium, calcium, and magnesium salts.
  • Salts derived from organic bases include, but are not limited to, salts of primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines and basic ion exchange resins, such as ammonia, isopropylamine, trimethylamine, diethylamine, triethylamine, tripropyl amine,
  • diethanolamine diethanolamine, ethanolamine, deanol, 2-dimethylaminoethanol, 2-diethylaminoethanol, dicyclohexylamine, lysine, arginine, histidine, caffeine, procaine, hydrabamine, choline, betaine, benethamine, benzathine, ethylenediamine, glucosamine, methylglucamine, theobromine, triethanolamine, tromethamine, purines, piperazine, piperidine,
  • N-ethylpiperidine polyamine resins and the like.
  • Particularly preferred organic bases are isopropylamine, diethylamine, ethanolamine, trimethylamine, dicyclohexylamine, choline and caffeine.
  • agent refers to a biological, pharmaceutical, or chemical compound.
  • Non-limiting examples include a simple or complex organic or inorganic molecule, a peptide, a protein, an oligonucleotide, an antibody, an antibody derivative, antibody fragment, a vitamin derivative, a carbohydrate, a toxin, and a chemotherapeutic compound.
  • Various compounds can be synthesized, for example, small molecules and oligomers (e.g., oligopeptides and oligonucleotides), and synthetic organic compounds based on various core structures.
  • various natural sources can provide compounds for screening, such as plant or animal extracts, and the like.
  • an "anti-cancer agent”, “anti-tumor agent” or “chemotherapeutic agent” refers to any agent useful in the treatment of a neoplastic condition.
  • One class of anti-cancer agents comprises chemotherapeutic agents.
  • “Chemotherapy” means the administration of one or more chemotherapeutic drugs to a subject by various methods, including intravenous, oral, intramuscular, intraperitoneal, intravesical, subcutaneous, transdermal, buccal, or inhalation or in the form of a suppository.
  • subject and “individual” are used interchangeably herein to refer to a vertebrate, preferably a mammal, more preferably a human.
  • Subject refers to an animal, such as a mammal, for example a human.
  • the methods described herein can be useful in both human therapeutics and veterinary applications.
  • the subject is a mammal, and in some embodiments, the subject is human.
  • Mammal includes humans and both domestic animals such as laboratory animals and household pets (e.g., cats, dogs, swine, cattle, sheep, goats, horses, rabbits), and non- domestic animals such as wildlife and the like. Mammals include, but are not limited to, murines, simians, humans, farm animals, sport animals, domesticated animals, and pets. Tissues, cells, and their progeny of a biological entity obtained in vivo or cultured in vitro are also encompassed.
  • in vivo refers to an event that takes place in a subject's body.
  • in vitro refers to an event that takes places outside of a subject's body.
  • an in vitro assay encompasses any assay run outside of a subject.
  • In vitro assays encompass cell-based assays in which cells alive or dead are employed.
  • In vitro assays also encompass a cell-free assay in which no intact cells are employed.
  • Prodrug is meant to indicate a compound that may be converted under physiological conditions or by solvolysis to a biologically active compound described herein (e.g., Ras antagonist).
  • the term “prodrug” encompasses a precursor of a biologically active compound that is pharmaceutically acceptable.
  • a prodrug is inactive when administered to a subject but is converted in vivo to an active compound, for example, by hydrolysis.
  • the prodrug compound often offers advantages of solubility, tissue compatibility or delayed release in a mammalian organism (see, e.g., Bundgard, H., Design of Prodrugs (1985), pp. 7-9, 21-24 (Elsevier, Amsterdam); Higuchi, T., et al., "Pro-drugs as Novel Delivery
  • prodrug is also meant to include any covalently bonded carriers, which release the active compound in vivo when such prodrug is administered to a mammalian subject.
  • Prodrugs of an active compound, as described herein are typically prepared by modifying functional groups present in the active compound in such a way that the modifications are cleaved, either in routine manipulation or in vivo, to the parent active compound.
  • Prodrugs include compounds wherein a hydroxy, amino or mercapto group is bonded to any group that, when the prodrug of the active compound is administered to a mammalian subject, cleaves to form a free hydroxy, free amino or free mercapto group, respectively.
  • Examples of prodrugs include, but are not limited to, acetate, formate and benzoate derivatives of a hydroxy functional group, or acetamide, formamide and benzamide derivatives of an amine functional group in the active compound and the like.
  • the proteins or compounds disclosed herein are isotopically labeled.
  • Isotopically-labeled proteins or compounds e.g., an isotopologue
  • isotopes that can be incorporated into the disclosed compounds include isotopes of hydrogen, carbon, nitrogen, oxygen, phosphorous, sulfur, fluorine, chlorine, and iodine, such as 2 H, 3 ⁇ 4 U C, 13 C, 14 C, 13 N, 15 N, 15 0, 17 0, 18 0, 31 P, 32 P, 35 S, 18 F, 36 C1, 123 I, and 125 I, respectively.
  • Certain isotopically-labeled compounds are useful in mass spectrometry studies. For instance, a stable isotopic protein may be used as a reference standard in a mass spectrometry based assay.
  • Certain isotopically- labeled compounds are useful in drug and/or substrate tissue distribution studies.
  • the radioactive isotopes tritium ( 3 H) and carbon- 14 ( 14 C) are particularly useful for this purpose in view of their ease of incorporation and ready means of detection.
  • These radiolabeled compounds could be useful to help determine or measure the effectiveness of the compounds, by characterizing, for example, the site or mode of action, or binding affinity to a pharmacologically important site of action.
  • substitution with heavier isotopes such as deuterium ( 2 H) may afford certain therapeutic advantages resulting from greater metabolic stability, for example, increased in vivo half-life or reduced dosage requirements, and hence are preferred in some circumstances.
  • Substitution with positron emitting isotopes such as 11 C, 18 F, 15 O and 13 N, can be useful in Positron Emission Topography (PET) studies for examining substrate receptor occupancy.
  • PET Positron Emission Topography
  • Isotopically-labeled compounds can generally be prepared by conventional techniques known to those skilled in the art or by processes analogous to those described herein using an appropriate isotopically-labeled reagent in place of the non-labeled reagent.
  • “Pharmaceutically acceptable carrier, diluent or excipient” includes without limitation any adjuvant, carrier, excipient, glidant, sweetening agent, diluent, preservative, dye, colorant, flavor enhancer, surfactant, wetting agent, dispersing agent, suspending agent, stabilizer, isotonic agent, solvent, or emulsifier which has been approved by the United States Food and Drug Administration as being acceptable for use in humans or domestic animals.
  • pharmaceutically acceptable salts may contain one or more asymmetric centers and may thus give rise to enantiomers, diastereomers, and other stereoisomeric forms that are defined, in terms of absolute stereochemistry, as (R)- or (S)- or, as (D)- or (L)- for amino acids.
  • the present disclosure is meant to include all such possible isomers, as well as their racemic and optically pure forms.
  • a "stereoisomer” refers to a compound made up of the same atoms bonded by the same bonds but having different three-dimensional structures, which are not interchangeable.
  • the present disclosure contemplates various stereoisomers and mixtures thereof and includes “enantiomers”, which refers to two stereoisomers whose molecules are nonsuperimposeable mirror images of one another.
  • Optically active (+) and (-), (R)- and (5)-, or (D)- and (L)- isomers may be prepared using chiral synthons or chiral reagents, or resolved using conventional techniques, for example, chromatography and fractional crystallization.
  • Conventional techniques for the preparation/isolation of individual enantiomers include chiral synthesis from a suitable optically pure precursor or resolution of the racemate (or the racemate of a salt or derivative) using, for example, chiral high pressure liquid
  • a "tautomer” refers to a proton shift from one atom of a molecule to another atom of the same molecule.
  • the present disclosure includes tautomers of any the compounds and all tautomeric forms are also intended to be included.
  • electrophile refers to any moiety capable of reacting with a nucleophile (e.g., a moiety having a lone pair of electrons, a negative charge, a partial negative charge and/or an excess of electrons, for example a -SH group).
  • Electrophiles typically are electron poor or comprise atoms which are electron poor.
  • an electrophile contains a positive charge or partial positive charge, has a resonance structure which contains a positive charge or partial positive charge, or is a moiety in which derealization or polarization of electrons results in one or more atoms which contain a positive charge or partial positive charge.
  • the electrophile comprises conjugated double bonds, for example an ⁇ , ⁇ - unsaturated carbonyl or ⁇ , ⁇ -unsaturated thiocarbonyl compound.
  • the electrophile is capable of covalent and/or irreversible binding to cysteine sulfhydryl groups.
  • the electrophile is capable of forming an irreversible covalent bond with a Ras protein, such as with a cysteine of a Ras protein.
  • a "ligand” as used herein refers to a small molecule, small molecule fragment, or biological polymer (e.g., polypeptide, nucleic acid, carbohydrate) that can selectively bind to a receptor.
  • the binding can be covalent or noncovalent.
  • selective refers to a binding interaction that is detectable over nonspecific interactions via a quantitative assay.
  • Alkyl refers to a straight or branched hydrocarbon chain moiety consisting solely of carbon and hydrogen atoms, which is saturated or unsaturated (i.e., contains one or more double and/or triple bonds), having from one to twelve carbon atoms (Ci-Co alkyl), preferably one to eight carbon atoms (Ci-C 8 alkyl) or one to six carbon atoms (Ci-C 6 alkyl), and which is attached to the rest of the molecule by a single bond, e.g., methyl, ethyl, ⁇ -propyl, 1 -methyl ethyl (z ' so-propyl), «-butyl, «-pentyl, 1,1 -dimethyl ethyl (t-butyl),
  • Alkyl includes alkenyls (one or more carbon-carbon double bonds) and alkynyls (one or more carbon-carbon triple bonds). Unless stated otherwise specifically in the specification, an alkyl group is optionally substituted.
  • Alkoxy refers to a moiety of the formula -OR a where R a is an alkyl group as defined herein containing one to twelve carbon atoms. Unless stated otherwise specifically in the specification, an alkoxy group is optionally substituted.
  • Alkylamino refers to a moiety of the formula - HR a or - R a R b where R a and R are each independently an alkyl group as defined herein containing one to twelve carbon atoms. Unless stated otherwise specifically in the specification, an alkylamino group is optionally substituted.
  • aminoalkyl refers to an alkyl moiety comprising at least one amino substituent.
  • the amino substituent can be on a tertiary, secondary or primary carbon. Unless stated otherwise specifically in the specification, an aminoalkyl group is optionally substituted.
  • Aryl refers to a hydrocarbon ring system moiety comprising 6 to 18 carbon atoms and at least one aromatic ring.
  • the aryl moiety is a
  • Aryl moieties include, but are not limited to, aceanthrylene, acenaphthylene, acephenanthrylene, anthracene, azulene, benzene, chrysene, fluoranthene, fluorene, as-indacene, s-indacene, indane, indene, naphthalene, phenalene, phenanthrene, pleiadene, pyrene, and triphenylene.
  • aryl is meant to include aryl groups that are optionally substituted.
  • Heterocycle refers to a saturated, unsaturated or aromatic ring comprising one or more heteroatoms.
  • exemplary heteroatoms include N, O, Si, P, B, and S atoms.
  • Heterocycles include 3- to 10-membered monocyclic rings, 6- to 12-membered bicyclic rings, and 6- to 12- membered bridged rings. Each ring of a bicyclic heterocycle may be selected from saturated, unsaturated, and aromatic rings.
  • the heterocycle may be attached to the rest of the molecule through any atom of the heterocycle, valence permitting, such as a carbon or nitrogen atom of the heterocycle.
  • the heterocycle is a heteroaryl.
  • the heterocycle is a heterocycloalkyl.
  • a heterocycle e.g., pyridyl
  • a saturated or unsaturated ring e.g., cyclohexane, cyclopentane, or cyclohexene.
  • exemplary heterocycles include pyrrolidinyl, pyrrolyl, imidazolyl, pyrazolyl, triazolyl, piperidinyl, pyridinyl, pyrimidinyl, pyridazinyl, pyrazinyl, thiophenyl, oxazolyl, thiazolyl, morpholinyl, indazolyl, indolyl, and quinolinyl.
  • a heterocycle is optionally substituted by one or more substituents such as those substituents described herein.
  • Heteroaryl refers to a 3- to 12-membered aromatic ring that comprises at least one heteroatom wherein each heteroatom may be independently selected from N, O, and S.
  • the heteroaryl ring may be selected from monocyclic or bicyclic and fused or bridged ring systems wherein at least one of the rings in the ring system is aromatic, i.e., it contains a cyclic, delocalized (4n+2) ⁇ -electron system in accordance with the Hiickel theory.
  • the heteroatom(s) in the heteroaryl may be optionally oxidized.
  • One or more nitrogen atoms, if present, are optionally quaternized.
  • heteroaryl may be attached to the rest of the molecule through any atom of the heteroaryl, valence permitting, such as a carbon or nitrogen atom of the heteroaryl.
  • heteroaryls include, but are not limited to, azepinyl, acridinyl, benzimidazolyl, benzindolyl, 1,3-benzodioxolyl, benzofuranyl, benzooxazolyl, benzo[d]thiazolyl, benzothiadiazolyl, benzo[£][l,4]dioxepinyl, benzo[b][l,4]oxazinyl, 1,4-benzodioxanyl, benzonaphthofuranyl, benzoxazolyl, benzodioxolyl, benzodioxinyl, benzopyranyl, benzopyranonyl, benzofuranyl, benzofuranonyl, benzothienyl
  • pyrazolo[3,4-d]pyrimidinyl pyridinyl, pyrido[3,2-d]pyrimidinyl, pyrido[3,4-d]pyrimidinyl, pyrazinyl, pyrimidinyl, pyridazinyl, pyrrolyl, quinazolinyl, quinoxalinyl, quinolinyl, isoquinolinyl, tetrahydroquinolinyl, 5,6,7,8-tetrahydroquinazolinyl, 5,6,7,8- tetrahydrobenzo[4,5]thieno[2,3-d]pyrimidinyl, 6,7,8, 9-tetrahydro-5H- cyclohepta[4,5]thieno[2,3-d]pyrimidinyl, 5,6,7,8-tetrahydropyrido[4,5-c]pyridazinyl, thiazolyl, thiadiazoly
  • thieno[3,2-d]pyrimidinyl thieno[2,3-c]pridinyl
  • thiophenyl i.e. thienyl
  • a heteroaryl is optionally substituted by one or more substituents such as those substituents described herein.
  • substituted refers to moieties having substituents replacing a hydrogen on one or more carbons or heteroatoms of the structure. It will be understood that “substitution” or “substituted with” includes the implicit proviso that such substitution is in accordance with permitted valence of the substituted atom and the substituent, and that the substitution results in a stable compound, e.g., which does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, etc. As used herein, the term “substituted” is contemplated to include all permissible substituents of organic compounds.
  • the permissible substituents include acyclic and cyclic, branched and unbranched, carbocyclic and heterocyclic, aromatic and non-aromatic substituents of organic compounds.
  • the permissible substituents can be one or more and the same or different for appropriate organic compounds.
  • the heteroatoms such as nitrogen may have hydrogen substituents and/or any permissible substituents of organic compounds described herein which satisfy the valences of the heteroatoms.
  • Substituents can include any of any permissible substituents of organic compounds described herein which satisfy the valences of the heteroatoms.
  • a halogen e.g., F, CI, Br, or I
  • a hydroxyl e.g., a carbonyl (such as a carboxyl, an alkoxycarbonyl, a formyl, or an acyl), a thiocarbonyl (such as a thioester, a thioacetate, or a thioformate), an alkoxyl, a phosphoryl, a phosphate, a phosphonate, a phosphinate, an amino, an amido, an amidine, an imine, a cyano, a nitro, an azido, a sulfhydryl, an alkylthio, a sulfate, a sulfonate, a sulfamoyl, a sulfonamido, a sulfonyl, a heterocyclyl, an aralkyl, a carbo
  • each R b is independently selected from a direct bond or a straight or branched alkylene, alkenylene, or alkynylene chain
  • each R c is a straight or branched alkylene, alkenylene or alkynylene chain.
  • a "competition binding assay” is a robust and high-throughput compatible assay strategy for screening against a specific binding site.
  • competition binding assays use a high affinity reversible ligand and employ fluorescence (e.g., fluorescence polarization, FRET), immunochemical (e.g., ELISA), or other detection methods (e.g., SPR, bead based methods) to determine the extent of ligand binding in the presence of competing molecules from a screening library.
  • fluorescence e.g., fluorescence polarization, FRET), immunochemical (e.g., ELISA), or other detection methods (e.g., SPR, bead based methods) to determine the extent of ligand binding in the presence of competing molecules from a screening library.
  • FRET fluorescence polarization
  • ELISA immunochemical
  • SPR bead based methods
  • covalent KRAS-G12C targeting compounds such as those described by Ostrem et al. (Ostrem, J.M.; Peters, U.; Sos, M.L.; Wells, J. A.; Shokat, K.M. Nature 2013, 503, 548-551, which is entirely incorporated herein by reference) may be used for competition binding assays.
  • Alternative 12-position mutants, such as G12V, G12D, and G12S are common in human cancers, and a preferred Ras screening strategy would allow for screening of multiple or all prominent Ras mutants.
  • Ras antagonists binding in the Switch II pocket may extend near the site of the 12-position and interact with the 12-position residue, providing some degree of mutant binding selectivity. Since mutant selective inhibitors would be a desired outcome of a screen, the ability to specifically screen the mutant of interest is likewise desirable. Flexibility in the screened target (e.g., the specific Ras mutant to be screened) is a feature of a preferred Ras screening assay.
  • the present disclosure provides a method of selecting a Ras antagonist.
  • An illustration of an exemplary embodiment is provided in Fig. 1.
  • the method comprises combining in a competition reaction a mutant Ras, a competition probe, and a test compound.
  • the method comprises detecting a decrease in binding between the mutant Ras and the competition probe as compared to binding of the mutant Ras in the absence of the test compound.
  • the competition probe comprises a reactive moiety, such as a nucleophilic group or an electrophilic group such as any electrophilic group capable of covalent and/or irreversible binding to a cysteine thiol roup.
  • the competition probe comprises a reactive moiety, such as a nucleophilic group or an electrophilic group such as any electrophilic group capable of covalent and/or irreversible binding to a cysteine thiol roup.
  • competition probe is a compound of formula , or a pharmaceutically acceptable salt thereof, wherein E comprises a reactive moiety, such as a nucleophilic group or an electrophilic group such as any electrophilic group capable of covalent and/or irreversible binding to a cysteine thiol group. Additional examples of competition probes are provided in Table 2 and Table 3. One or more competition probes may be used in a single reaction. For example, a competition reaction may comprise 1, 2, 3, 4, 5, or more
  • the competition probe is selected from the group consisting of CP-001, CP-002, CP-003, CP-004, CP-005, CP-006, CP-007, CP-008, CP-009, CP-010, CP-011, CP-012, CP-013, CP-014, CP-015, CP-016, CP-017, CP-018, CP-019,CP- 020, and any combination thereof.
  • the competition probe binds to Ras with a 3 ⁇ 4 of about or at least about 100 pM, 200 pM, 300 pM, 400 pM, 500 pM, 600 pM, 700 pM, 800 pM, 900 pM, 1 nM, 2 nM, 3 nM, 4 nM, 5 nM, 6 nM, 7 nM, 8 nM, 9 nM, 10 nM, 15 nM, 20 nM, 25 nM, 30 nM, 35 nM, 40 nM, 45 nM, 50 nM, 55 nM, 60 nM, 65 nM, 70 nM, 75 nM, 80 nM, 85 nM, 90 nM, 95 nM, 100 nM, 150 nM, 200 nM, 250 nM, 300 nM, 350 nM, 400 nM, 450 nM, 500 nM,
  • the competition probe binds to Ras with a K d of up to about 100 pM, 200 pM, 300 pM, 400 pM, 500 pM, 600 pM, 700 pM, 800 pM, 900 pM, 1 nM, 2 nM, 3 nM, 4 nM, 5 nM, 6 nM, 7 nM, 8 nM, 9 nM, 10 nM, 15 nM, 20 nM, 25 nM, 30 nM, 35 nM, 40 nM, 45 nM, 50 nM, 55 nM, 60 nM, 65 nM, 70 nM, 75 nM, 80 nM, 85 nM, 90 nM, 95 nM, 100 nM, 150 nM, 200 nM, 250 nM, 300 nM, 350 nM, 400 nM, 450 nM, 500 nM, 550 nM
  • the competition probe covalently modifies a mutant Ras.
  • Covalent modification can be expressed as a percentage of modified protein. The percentage of protein modified may be calibrated based on reaction conditions, such as the competition probe selected, the Ras mutant under study, the concentration of the competition probe, and the duration of the reaction. In some embodiments, the competition probe covalently modifies a percentage of mutant Ras proteins in a competition reaction, control reaction, or reaction mixture.
  • the competition probe covalently modifies about or at least about 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% of mutant Ras proteins in a competition reaction, control reaction, or reaction mixture.
  • the competition probe covalently modifies up to about 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% of mutant Ras proteins in a competition reaction, control reaction, or reaction mixture.
  • a control reaction such as a reaction comprising a competition probe and a mutant Ras in the absence of one or more test compounds, can form a baseline for comparing the effects of competition with one or more test compounds.
  • a competition probe is provided at a concentration of at least about 5 ⁇ (e.g., 10 ⁇ , 30 ⁇ , 100 ⁇ , or more), and achieves at least about 80% modification (e.g., 85%, 90%, 95%, or higher) in about or fewer than about 10 hours (e.g., 8, 7, 6, 5, 4, 3, 2, or fewer hours) in the absence of a test compound.
  • covalent e.g., 85%, 90%, 95%, or higher
  • modification in the presence of a test compound is expressed as a percentage relative to the degree of modification obtained in a control reaction lacking the test compound.
  • the presence of a test compound may reduce covalent modification of a mutant Ras by about or at least about 10%, 25%, 50%, 75%, 90%, or more relative to the control reaction.
  • a test compound is selected from the group consisting of CP- 023 (l-(4-(6-chloro-2-(3-(dimethylamino)propoxy)-8-fluoro-7-(3-hydroxynaphthalen-l- yl)quinazolin-4-yl)piperazin-l-yl)ethanone), CP-024 (4-(6-chloro-2-(3- (dimethylamino)propoxy)-8-fluoro-7-(3-hydroxynaphthalen-l-yl)quinazolin-4-yl)piperazine- 1-carb aldehyde), and any combination thereof.
  • Ras mutants useful in the methods and compositions of the disclosure can comprise one or more mutations, such as any of the mutant Ras proteins described herein. Mutations may be naturally occurring mutations, or mutations that are artificially generated, such as by non-specific or targeted mutagenesis procedures. Examples of mutations that can be introduced include, but are not limited to, insertions, deletions, substitutions, and
  • the mutation is a substitution, such as in the substitution of an amino acid.
  • the positions for substituted amino acid introduction may be chosen to be near enough to the Switch II pocket to allow for reaction with a Switch II binding competition probe, but outside of the pocket so as not to alter the binding properties of Switch II pocket binders (see e.g., Fig. 2).
  • positions may be selected that show some degree of variation across small GTPase sequence space, as shown in Fig. 3 and Fig. 4.
  • many positions in the core small GTPase fold are invariant across the entire family.
  • a cysteine mutation may be a mutation relative to position 62, 92, or 95 of SEQ ID NO: 1 when optimally aligned.
  • cysteine mutations are cysteine mutations.
  • the cysteine mutation is not at position 12 or 13 relative to SEQ ID NO: 1 when optimally aligned. In some embodiments, the cysteine mutation is at position 12 or 13 relative to SEQ ID NO: 1 when optimally aligned. In some embodiments, the cysteine mutation is at position 12 or 13 relative to SEQ ID NO: 1 when optimally aligned, and the mutant Ras is selected from mutant MRAS, mutant ERAS, mutant RRAS2, mutant RALA, mutant RALB, mutant RIT1, and any combination thereof. In some embodiments, the cysteine mutation is at a non-conserved amino acid position.
  • a “conserved amino acid” refers to an amino acid that is either identical or functionally or structurally equivalent at analogous positions across homologous species or members of a protein family. Where an identical amino acid or functionally or structurally equivalent amino acid is found in at least 2, 3, 4, 5, or more members of a family, such amino acid can be considered as highly conserved. Examples of conserved amino acids are provided herein, and others are recognized in the art.
  • the competition probe covalently modifies the mutant Ras by reacting with the cysteine residue of the cysteine mutation. Modification may be selective, such as by selectively binding the mutant Ras (e.g., in proximity to a cysteine residue to be modified).
  • the cysteine mutation is a mutation relative to SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, or SEQ ID NO: 26 when optimally aligned.
  • the cysteine mutation is at position 62, 92, 95, or any combination thereof relative to SEQ ID NO: 1 when optimally aligned.
  • the mutant Ras comprises one or more additional mutations.
  • the mutant Ras comprises 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more additional mutations.
  • the additional mutations may comprise one or more cysteine mutations.
  • the additional mutations do not comprise cysteine mutations.
  • Non-limiting examples of additional mutations include substitutions, deletions, and insertions.
  • a mutant Ras comprises a mutation at one or more of positions 12, 13, 14, 18, 19, 22, 59, 60, 61, 63, 117, and 146 relative to SEQ ID NO: 1 when optimally aligned. In some embodiments, the mutant Ras comprises a mutation at one or more of positions 12, 13, 18, 61, 117, and 146 relative to SEQ ID NO: 1 when optimally aligned.
  • a mutant Ras may comprise a mutation at one or both of positons 12 and 13 relative to SEQ ID NO: 1 when optimally aligned (e.g., an aspartic acid at position 12 and/or 13 relative to SEQ ID NO: 1 when optimally aligned). Exemplary Ras and mutant Ras sequences are provided in Table 1.
  • a competition reaction comprises, in addition to a competition probe, one or more test compounds (e.g., 1, 2, 3, 4, 5, 10, 25, 50, or more test compounds).
  • Test compounds may be drawn from a library of test compounds, such as a library of 100, 1000, 5000, 10000, 50000, 100000, or more compounds.
  • a test compound that competes for binding with the competition probe is identified as binding to the mutant Ras.
  • the test compound may interact with Ras via a chemical bond selected from the group consisting of a hydrogen bond, van der Waals interaction, ionic bond, covalent bond, hydrophobic interaction, and any combination thereof.
  • the test compound interacts with the Switch II binding pocket of Ras.
  • the degree of competition with the competition probe is indicative of affinity of a test compound for the mutant Ras.
  • the test compound binds to Ras with a K d of about or at least about 100 pM, 200 pM, 300 pM, 400 pM, 500 pM, 600 pM, 700 pM, 800 pM, 900 pM, 1 nM, 2 nM, 3 nM, 4 nM, 5 nM, 6 nM, 7 nM, 8 nM, 9 nM, 10 nM, 15 nM, 20 nM, 25 nM, 30 nM, 35 nM, 40 nM, 45 nM, 50 nM, 55 nM, 60 nM, 65 nM, 70 nM, 75 nM, 80 nM, 85 nM, 90 nM, 95 nM, 100 nM, 150 nM, 200 nM, 250 nM, 300 nM
  • the test compound binds to Ras with a 3 ⁇ 4 of up to about 100 pM, 200 pM, 300 pM, 400 pM, 500 pM, 600 pM, 700 pM, 800 pM, 900 pM, 1 nM, 2 nM, 3 nM, 4 nM, 5 nM, 6 nM, 7 nM, 8 nM, 9 nM, 10 nM, 15 nM, 20 nM, 25 nM, 30 nM, 35 nM, 40 nM, 45 nM, 50 nM, 55 nM, 60 nM, 65 nM, 70 nM, 75 nM, 80 nM, 85 nM, 90 nM, 95 nM, 100 nM, 150 nM, 200 nM, 250 nM, 300 nM, 350 nM, 400 nM, 450 nM, 500 nM, 550 nM
  • the test compound binds to a GDP -bound Ras protein with a K d of at most 100 ⁇ , thereby antagonizing Ras activity.
  • Antagonizing Ras activity can be measured in a variety of ways, with respect to one or more of Ras functions or downstream effects.
  • Non-limiting examples of Ras activity that may be antagonized by a test compound include modulation of GTPase activity, nucleotide exchange, effector protein binding, effector protein activation, guanine exchange factor (GEF) binding, GEF-facilitated nucleotide exchange, phosphate release, nucleotide release, nucleotide binding, Ras subcellular localization, Ras post-translational processing, or Ras post-translational modification.
  • the test compound inhibits the binding or release of GDP or GTP to a Ras protein.
  • a decrease in binding between the mutant Ras and the competition probe in the presence of one or more test compounds is indicative of Ras antagonist activity of the one or more test compounds.
  • a test compound associated with such a decrease in competition probe binding may be selected as a Ras antagonist.
  • a test compound is selected as a Ras antagonist if competition probe binding is reduced by at least a specified threshold degree (e.g., expressed as a percentage). The decrease in binding may be measured with respect to a control reaction, such as a reaction comprising the same concentrations of competition probe and mutant Ras reacted for the same amount of time but lacking any test compound.
  • the decrease in binding between the mutant Ras and the competition probe is about or at least about 5, 10, 25, 50, 75, 80, 85, 90, 95, 96, 97, 98, 99, or 100%. In some embodiments, the decrease in binding between the mutant Ras and the competition probe is at least about 75%.
  • Degree of binding between a competition probe and a mutant Ras can be measured by any suitable method.
  • the method selected may depend on the nature of the modification to the mutant Ras (e.g., addition of a detectable label and/or formation of a complex between the mutant Ras and the competition probe).
  • a Ras, mutant Ras, or competition probe can be conjugated to a detectable label.
  • Suitable detectable labels can include any composition detectable by photochemical, biochemical, spectroscopic, immunochemical, electrical, optical, or chemical means.
  • a wide variety of appropriate detectable labels are known in the art, which include fluorescent labels, chemiluminescent labels, radioactive isotope labels, stable isotope labels, enzymatic labels, and ligands.
  • Detectable labels can be added to competition probes or test compounds by any well- known chemical method that does not ablate compound binding. This can be ascertained by identifying positions on the compound scaffold that contact solvent in an appropriate x-ray crystal structure (such as Fig. 2), or by identifying positions on a molecule where the addition of lengthy substituents does not dramatically affect the ability of the compound to bind to Ras, and by conjugating the detectable label to the core directly or indirectly.
  • appropriate positions for conjugation include (but are not limited to) the 4-position nitrogen of the piperazinyl moiety occupied by Rl or the 2-position carbon of the quinazolyl moiety.
  • a competition probe or test compound has a structure of Formula I: (Formula I),
  • Ri is selected from the group consisting of H, alkyl, substituted alkyl, acyl, heterocycle, substituted heterocycle, aryl, substituted aryl, heteroaryl, substituted heteroaryl, and any combination thereof;
  • R 2 is selected from the group consisting of H, alkyl, substituted alkyl, heteroalkyl, substituted heteroalkyl, alkoxy, amino, aminoalkyl, alkylamino, heterocycle, substituted heterocycle, aryl, substituted aryl, heteroaryl, substituted heteroaryl, and any combination thereof;
  • each of R 3 , R 4 , R5, and 5 is independently selected from the group consisting of H, alkyl, substituted alkyl, halogen, hydroxyl, cyano, heterocycle, substituted heterocycle, aryl, substituted aryl, heteroaryl, substituted heteroaryl, and any combination thereof.
  • the heterocycle, substituted heterocycle, aryl, substituted aryl, heteroaryl, or substituted heteroaryl of Ri, R 2 , R3, R4, R5, and/or 5 is a 5- or 6-membered ring.
  • the substituted heterocycle, substituted aryl, or substituted heteroaryl of Ri, R 2 , R3, R 4 , R5, and/or R 6 is substituted with one or more substituents selected from the group consisting of alkyl, substituted alkyl, halogen, hydroxyl, cyano, and any combination thereof.
  • Ri or R 2 is conjugated to a detectable label or comprises an
  • the electrophile is selected from a 0
  • Ri is selected from the group consisting of H, alkyl substituted alkyl, acyl, and any combination thereof. In some embodiments, Ri is or
  • R 2 is selected from the group consisting of H, heteroalkyl, substituted heteroalkyl, alkoxy, amino, aminoalkyl, alkylamino, heterocycle, substituted heterocycle, and any combination thereof.
  • R 3 is selected from the group consisting of H, alkyl, substituted alkyl, halogen, hydroxyl, cyano, and any combination thereof. In some embodiments, R 3 is H.
  • R 4 is selected from the group consisting of H, CI,
  • R 5 is selected from the group consisting of H, halogen (e.g.,
  • R 6 is H or halogen (e.g., F).
  • a compound of Formula I is represented by a structure of Formula II:
  • R 7 is selected from the group consisting of H, alkyl, substituted alkyl, and any combination thereof;
  • R 8 is selected from the group consisting of H, alkyl, substituted alkyl, heterocycle, substituted heterocycle, aryl, substituted aryl, heteroaryl, substituted heteroaryl, and any combination thereof.
  • a compound of Formula I is represented by a structure of Formula III:
  • R 7 is selected from the group consisting of H, alkyl, substituted alkyl, and any combination thereof;
  • R is selected from the group consisting of H, alkyl, substituted alkyl, heteroalkyl, substituted heteroalkyl, alkoxy, amino, aminoalkyl, alkylamino, heterocycle, substituted heterocycle, aryl, substituted aryl, heteroaryl, substituted heteroaryl, and any combination thereof.
  • R 9 is selected from the group consisting of H, heteroalkyl, substituted heteroalkyl, alkoxy, amino, aminoalkyl, alkylamino, heterocycle, substituted heterocycle, and any combination thereof.
  • a compound of Formula I is represented by a structure of Formula IV:
  • Rio is selected from the group consisting of H, alkyl, substituted alkyl, heterocycle, substituted heterocycle, aryl, substituted aryl, heteroaryl, substituted heteroaryl, and any combination thereof.
  • a compound of Formula I is represented by a structure of Formula V:
  • Rii is selected from the group consisting of H, alkyl, substituted alkyl, heterocycle, substituted heterocycle, aryl, substituted aryl, heteroaryl, substituted heteroaryl, and any combination thereof.
  • a compound of Formula I is represented by a structure of Formula VI:
  • Ri2 is selected from the group consisting of H, alkyl, substituted alkyl, heterocycle, substituted heterocycle, aryl, substituted aryl, heteroaryl, substituted heteroaryl, and any combination thereof.
  • Ri, R 2 , R 7 , R 8 , Rs>, Rio, Rii, or R i2 is conjugated to a detectable label or comprises an electrophile.
  • a compound of Formula I, II, III, IV, V, or VI is conjugated to a detectable label.
  • reaction times and conditions are intended to be approximate, e.g., taking place at about atmospheric pressure within a temperature range of about -10 °C to about 110 °C over a period of about 1 to about 24 hours; reactions left to run overnight average a period of about 16 hours.
  • a competition probe or test compound of Formula III is accessed s nthetically by scheme A:
  • a competition probe or test compound of Formula IV is accessed synthetically by scheme B:
  • a competition probe or test compound of formula V is accessed synthetically by scheme C:
  • Detectable labels can be added to Ras mutants by any of a variety of chemical methods that do not disrupt protein folding/activity.
  • detectable labels are conjugated to cysteines on Ras via reaction with an appropriate maleimide-conjugated probe in the presence of tris(carboxyethyl)phosphine (TCEP) in a buffer solution at physiological pH.
  • detectable labels are conjugated to lysines on Ras via reaction with an appropriate N-hydroxysuccinimide ( HS)-conjugated probe in 0.1M sodium carbonate buffer solution.
  • detectable labels are conjugated to Ras by: a) first translating Ras in the presence of L-Azidohomoalanine or L- homopropargylglycine (both incorporated at the site of methionine residues) to produce a Ras incorporating unnatural amino acid residues, and b) reacting the unnatural amino acid residue bearing Ras with azide- or alkyne-derivatized detectable probes under suitable "click" chemistry reaction conditions.
  • Fluorescent labels include both protein and non-protein organic fluorophores, as well as organometallic fluorophores.
  • Protein fluorophores known to those of skill in the art include green fluorescent proteins (GFPs, fluorescent proteins that fluoresce in the green region of the spectrum, generally emitting light having a wavelength from 500-550 nanometers), cyan-fluorescent proteins (CFPs, fluorescent proteins that fluoresce in the cyan region of the spectrum, generally emitting light having a wavelength from 450-500 nanometers), red fluorescent proteins (RFPs, fluorescent proteins that fluoresce in the red region of the spectrum, generally emitting light having a wavelength from 600-650 nanometers).
  • GFPs green fluorescent proteins
  • CFPs cyan-fluorescent proteins
  • RFPs red fluorescent proteins
  • protein fluorophores known to those in the art additionally include mutants and spectral variants of these proteins that retain their fluorescent properties, of which non-limiting examples are AcGFP, AcGFPl, AmCyan, AmCyanl, AQ143, AsRed2, Azami Green, Azurite, BFP, Cerulean, CFP, CGFP, Citrine, copGFP, CyPet, dKeima-Tandem, DsRed, dsRed-Express, DsRed-Monomer, DsRed2, dTomato, dTomato-Tandem, EBFP, EBFP2, ECFP, EGFP, Emerald, EosFP, EYFP, GFP, HcRed-Tandem, HcRedl, JRed, Katuska, Kusabira Orange, Kusabira Orange2, mApple, mBanana, mCerulean, mCFP, mCherry,
  • phycobiliproteins and fragments of phycobiliproteins of which non-limiting examples are A- phycoerythrin, B-phycoerythrin, C-phycocyanin, allophycocyanin, XL665, or d2.
  • Nonprotein organic fluorophores known to those of skill in the art include, but are not limited to, xanthene derivatives (of which common examples are fluorescein, rhodamine, Oregon green, eosin, and texas red), cyanine derivatives (of which common examples are cyanine, indocarbocyanine, oxacorbocyanine, thiacarbocyanine, and merocyanine), squaraine derivatives (of which common examples are Seta, SeTau, and Square dyes), naphthalene derivatives (of which common examples are dansyl and prodan), coumarin derivatives, oxadiazole derivatives (of which common examples are pyridyloxazole, nitrobenzoxadiazole, and benzoxadiazole), anthracene derivatives (of which common examples are anthraquinones such as DRAQ5, DRAQ7, and CyTRAK Orange), pyrene derivatives (of which a common examples
  • Non-protein organic fluorophores also include the near-IR HTRF acceptor d2.
  • Organometallic fluorophores include lanthanide ion chelates, nonlimiting examples of which include tris(dibenzoylmethane) mono(l,10- phenanthroline)europium(lll), tris(dibenzoylmethane) mono(5 -amino- 1, 10- phenanthroline)europium (111), and Lumi4-Tb cryptate.
  • Chemiluminescent labels include enzymes of the luciferase class, which produce light upon combination with suitable substrates and cofactors. There are variety of commercially used recombinant luciferases with different primary sequences and different cofactor requirements. Non-limiting examples include Cypridina, Gaussia, Renilla, and Firefly luciferases.
  • Enzymatic labels include horseradish peroxidase (HRP), alkaline phosphatase (AP), beta-galactosidase, glucose oxidase, and other well known labels.
  • HRP horseradish peroxidase
  • AP alkaline phosphatase
  • beta-galactosidase beta-galactosidase
  • glucose oxidase glucose oxidase
  • detection reagents which are compositions comprising a substrate which produces a detectable signal upon reaction with the enzyme in the detection zone.
  • the detectable signal may be colorimetric or luminescent.
  • HRP produces blue light when reacted with luminol in the presence of H 2 0 2 .
  • AP produces a yellow reaction product when combined with p-nitrophenyl phosphate (pNPP).
  • Enzymatic labels may be conjugated to amino or sulfhydryl groups of Ras by methods similar to those used to conjugate them to antibodies. Such methods include crosslinking using glutaraldehyde or 2-step crosslinking using heterobifunctional crosslinkers such as succinimidyl 4-(N-maleimidomethyl)cyclohexane-l-carboxylate (SMCC) or sulfosuccinimidyl 4-(N-maleimidomethyl)cyclohexane-l-carboxylate (sulfo-SMCC).
  • SMCC N-maleimidomethylcyclohexane-l-carboxylate
  • sulfo-SMCC sulfo-SMCC
  • Radioactive isotope labels include, but are not limited to, 3 H, 14 C, 22 Na, 32 P, 33 P, 35 S, 42 K, 45 Ca, 59 Fe, 125 1, 203 Hg, or the like.
  • Such radioactive isotope labels can either be conjugated to a small molecule or protein of the invention or incorporated into the explicit structure of a protein or a small molecule of the invention.
  • amino groups on proteins or small molecules can be reacted with 14 C-paraformaldehyde followed by sodium cyanoborohydride to add a detectable 14 C-methyl group via reductive amination.
  • a protein may be translated in the presence of 35 S- methionine to produce a protein with a detectable 35 S atom at the site of methionine residues.
  • Stable isotope labels suitable for detection comprise chemical moieties incorporating
  • a protein can be translated in the presence of 13 C-arginine (to produce a protein containing a detectable 13 C atom at the sites of arginine residues), or a small molecule synthetic step utilizing acetic anhydride can instead substitute 13 C-acetic anhydride to produce a molecule having a detectable 13 C atom at the site of an existing acetyl group.
  • acetic anhydride can instead substitute 13 C-acetic anhydride to produce a molecule having a detectable 13 C atom at the site of an existing acetyl group.
  • Many general synthetic methods in commercial and research use for stable isotope labeling are also useful for radioactive isotope labeling, and vice versa.
  • Ligands suitable for detection are those for which a well-characterized receptor partner is available, and the ligand-receptor interaction serves to detect or isolate the ligand.
  • the ligand/receptor pair can be either natural or non-natural.
  • Non-limiting examples of natural ligand-receptor pairs include maltose/maltose binding protein (MBP),
  • GST glutathione/glutathione-S-transferase
  • calmodulin/calmodulin binding protein IgG/protein G, IgG/protein A, and biotin/streptavidin.
  • non-natural ligand/receptor pairs include polyhistidine/Ni-nitriloacetic acid(NTA), FLAG peptide/anti- FLAG antibody.
  • the ligand/receptor pair can also comprise two small molecule fragments, as in the case of "click" reaction pairs such as azide/alkyne (Huisgen cycloaddition), azide/cyclooctyne (Huisgen cycloaddition), or azide with phosphine or phosphite (Staudinger ligation).
  • radiolabels e.g., radioactive isotope labels
  • Stable isotope labels e.g., 13 C-acetyl
  • MR nuclear magnetic resonance
  • MS mass spectrometry
  • Fluorescent labels e.g., fluorescent dyes, fluorescent proteins
  • each of a plurality of probes in a single reaction is conjugated to a different detectable label (e.g., fluorescent dyes with different emission spectra), such that the signal corresponding to different targets can be differentiated.
  • fluorescent dyes used as detectable labels have overlapping emission and absorption spectra such that binding or proximity of elements conjugated to the fluorescent dyes can be detected by Forster resonance energy transfer (FRET).
  • FRET Forster resonance energy transfer
  • Enzymatic labels are typically detected by providing the enzyme with a substrate and measuring the reaction product produced by the action of the enzyme on the substrate. Colorimetric labels are typically detected by visualizing the colored label or are quantified using a spectrophotometer. In some embodiments, binding to or modification by a competition probe is measured by mass spectrometry.
  • Competition probes may carry a label to facilitate their detection.
  • the label is a fluorescent label.
  • the detectable label need not be a fluorescent label. Any label can be used which allows the detection of the binding of the competition probe to a mutant Ras or the covalent modification of a mutant Ras by a competition probe.
  • One method for detecting a fluorescently labeled competition probe comprises using laser light of a wavelength specific for the labeled competition probe, or the use of other suitable sources of illumination. Fluorescence from the label on a competition probe may be detected by a CCD camera or other suitable detection means.
  • the mutant Ras proteins and competition probes described herein can be used for competition binding assays to screen for reversible binders to the Switch II pocket of Ras.
  • An exemplary illustration in accordance with an embodiment is shown in Fig. 1.
  • mass spectrometry based assays are performed by evaluating the protein- ligand complex or by monitoring the depletion of the competition probe in the presence of excess protein.
  • automated high throughput solid phase extraction- mass spectrometry platforms e.g., Agilent RapidFire
  • Agilent RapidFire may be used to enable screening of large libraries of test compounds (e.g libraries of more than 100,000 compounds).
  • additional assay formats such as fluorescence polarization or FRET may be used.
  • Modification of the competition probes with an affinity tag may enable additional assay formats such as ELISA or AlphaScreen.
  • the disclosure provides a method of producing a Ras antagonist.
  • the method comprises selecting the Ras antagonist according to any of the methods described herein, and synthesizing the compound.
  • Compounds can be synthesized according to any suitable process.
  • Compounds identified as Ras antagonists according to a method disclosed herein may be further tested to assess effects on one or more Ras activities, examples of which are described above.
  • Compounds may also be prepared for use in treating a mutant-Ras-mediated condition of an individual.
  • the disclosure provides a pharmaceutical composition comprising a Ras antagonist or pharmaceutically acceptable salt thereof selected according to any of the methods described herein.
  • the compositions and methods of the present disclosure may be utilized to treat an individual in need thereof.
  • the individual is a mammal such as a human, or a non-human mammal.
  • the composition or the compound When administered to an animal, such as a human, the composition or the compound is preferably administered as, or formulated for administration as, a pharmaceutical composition comprising, for example, a Ras antagonist or pharmaceutically acceptable salt thereof selected according to any of the methods, kits, systems, or computer-readable medium described herein and a pharmaceutically acceptable carrier.
  • a Ras antagonist according to the present disclosure may be administered to an individual by any suitable route of administration, which route may depend on the nature of the formulation. Suitable routes of administration include, but are not limited to, oral, intravenous, rectal, aerosol, parenteral, ophthalmic, pulmonary, transmucosal, transdermal, vaginal, otic, nasal, and topical administration.
  • parenteral delivery includes intramuscular, subcutaneous, intravenous, intramedullary injections, as well as intrathecal, direct intraventricular, intraperitoneal, intralymphatic, and intranasal injections.
  • the pharmaceutical composition is formulated for oral administration.
  • the pharmaceutical composition is formulated for injection.
  • the pharmaceutical compositions comprise a compound as disclosed herein and an additional therapeutic agent (e.g., anticancer agent). Non-limiting examples of such therapeutic agents are described herein below.
  • a pharmaceutical composition is a mixture of a Ras antagonist or pharmaceutically acceptable salt thereof selected according to any of the methods, kits, systems, or computer-readable medium described herein and a pharmaceutically acceptable carrier with other chemical components, such as carriers, stabilizers, diluents, dispersing agents, suspending agents, thickening agents, and/or excipients.
  • the pharmaceutical composition facilitates administration of the compound to an organism. In some embodiments, practicing the methods of treatment or use provided herein,
  • therapeutically effective amounts of a Ras antagonist or pharmaceutically acceptable salt thereof selected according to any of the methods, kits, systems, or computer-readable medium described herein are administered in a pharmaceutical composition to a mammal having a disease, disorder or medical condition to be treated.
  • the mammal is a human.
  • therapeutically effective amounts vary depending on one or more of a variety of factors, including but not limited to, the severity of the disease, the age and relative health of the subject, the potency of the compound used and other factors.
  • a Ras antagonist or pharmaceutically acceptable salt thereof selected according to any of the methods, kits, systems, or computer-readable medium described herein and a pharmaceutically acceptable carrier may be used singly or in combination with one or more therapeutic agents as components of mixtures.
  • the disclosure provides a reaction mixture comprising one or more mutant Ras, one or more competition probe that is capable of binding the mutant Ras, and one or more test compounds.
  • the mutant Ras can be any mutant Ras described herein.
  • the one or more competition probe can be any competition probe described herein, including combinations of two or more competition probes (e.g., about 1, 2, 3, 4, 5, 10, 15, 25, 50, or more competition probes).
  • the one or more test compound can be any of a variety of test compounds, including one or more test compounds from a library of compounds (e.g., about 1, 2, 3, 4, 5, 10, 15, 25, 50, or more test compounds from a library of 1000, 10000, 50000, 100000, or more compounds).
  • the mutant Ras comprises a cysteine mutation; the competition probe is capable of covalently modifying the mutant Ras at the cysteine mutation; and the test compound inhibits covalent modification of the mutant Ras by the competition probe.
  • Reaction mixtures can comprise one or more elements disclosed herein in relation to any of the various aspects, in any combination.
  • the competition probe competes for binding in the Switch II pocket of the mutant Ras.
  • the cysteine mutation is not at position 12 or 13 relative to SEQ ID NO: 1 when optimally aligned.
  • the cysteine mutation is a mutation relative to position 12 or 13 of SEQ ID NO: 1 when optimally aligned.
  • the cysteine mutation is at position 12 or 13 relative to SEQ ID NO: 1 when optimally aligned, and the mutant Ras is selected from mutant MRAS, mutant ERAS, mutant RRAS2, mutant RALA, mutant RALB, mutant RITl, and any combination thereof.
  • the cysteine mutation is at a non-conserved amino acid position.
  • the cysteine mutation is a mutation relative to position 62, 92, or 95 of SEQ ID NO: 1 when optimally aligned.
  • the mutant Ras comprises one or more additional mutations.
  • the test compound interacts with Ras via a chemical bond selected from the group consisting of a hydrogen bond, van der Waals interaction, ionic bond, covalent bond, hydrophobic interaction, and any combination thereof. In some embodiments, the test compound interacts with the Switch II binding pocket of Ras.
  • reaction parameters in a competition reaction, control reaction, or reaction mixture such as order of addition, temperature, reaction duration or time, quantity or identity of reaction components (e.g., mutant Ras, competition probe, test compound), concentration (e.g., concentration of mutant Ras, concentration of competition probe, concentration of test compound), stoichiometry (e.g., ratio of competition probe to mutant Ras, ratio of test compound to mutant Ras, ratio of test compound to competition probe), buffer composition, pH, and reaction site can be adjusted.
  • One or more reaction parameters may be adjusted to affect the extent of reaction (e.g., binding or covalent modification).
  • a mutant Ras, competition probe, and test compound can be added simultaneously or sequentially in any order to a competition reaction or reaction mixture.
  • a mutant Ras and competition probe can be added simultaneously or sequentially in any order to a competition reaction, control reaction, or reaction mixture.
  • a competition reaction, control reaction, or reaction mixture may include multiple steps, including but not limited to binding, reaction, covalent modification, mixing, heating, cooling, denaturation, and regeneration. Steps in a competition reaction, control reaction, or reaction mixture can comprise any temperature or gradient of temperatures, suitable for achieving the purpose of the given step. Suitable temperatures may include, but are not limited to, room temperature; about 10, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, and 40 °C; and higher.
  • Steps in a competition reaction, control reaction, or reaction mixture may be of any duration, suitable for achieving the purpose of the given step. Suitable durations may include, but are not limited to, about 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, and 55 seconds; 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, and 55 minutes; and 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, and more hours, including indefinitely until manually interrupted.
  • the competition probe is selected in accordance with one or more parameters disclosed herein.
  • a competition probe may be selected such that in the absence of test compound about or at least about 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% of mutant Ras is bound or covalently modified (e.g., at a substituted amino acid such as a cysteine mutation).
  • a substituted amino acid such as a cysteine mutation
  • a competition probe may be selected such that in the absence of test compound up to about 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% of mutant Ras is bound or covalently modified (e.g., at a substituted amino acid such as a cysteine mutation).
  • a control reaction such as a reaction comprising a competition probe and a mutant Ras in the absence of one or more test compounds, can form a baseline for comparing the effects of competition with one or more test compounds.
  • a competition probe is provided at a concentration of at least about 5 ⁇ (e.g., 10 ⁇ , 30 ⁇ , 100 ⁇ , or more), and achieves at least about 80% modification (e.g., 85%, 90%, 95%, or higher) in about or fewer than about 10 hours (e.g., 8, 7, 6, 5, 4, 3, 2, or fewer hours) in the absence of a test compound.
  • a competition reaction, control reaction, or reaction mixture may comprise one or more mutant Ras proteins.
  • a competition reaction, control reaction, or reaction mixture may comprise about 1, 2, 3, 4, 5, 10, 15, 25, 50, or more mutant Ras proteins.
  • a competition reaction, control reaction, or reaction mixture may comprise all Ras mutants with a proteinogenic amino acid mutation at one or more positions, for example, by site saturation mutagenesis.
  • site saturation mutagenesis is performed at one or more positions selected from position 12, 13, 14, 18, 19, 22, 59, 60, 61, 63, 117, 146, and any combination thereof relative to SEQ ID NO: 1 when optimally aligned, such as from position 12, 13, 18, 61, 146, and any combination thereof.
  • Assays for assessing binding with a plurality of different Ras mutants may be performed in parallel, with each Ras mutant in a separate reaction mixture.
  • concentrations of various components of a reaction mixture can be selected for suitability under a given set of conditions.
  • concentration of a mutant Ras in a competition reaction, control reaction, or reaction mixture can be about or more than about 5 ⁇ , 10 ⁇ , 30 ⁇ , 100 ⁇ , 200 ⁇ , 500 ⁇ , 1 mM or more.
  • concentration of the mutant Ras may be selected based on the concentration of the competition probe, or vice versa.
  • the mutant Ras may be present at a 1-fold, 2-fold, 3-fold, 4-fold, 5-fold, 10-fold, 25-fold, or more excess relative to the concentration of the competition probe.
  • the concentration of a competition probe in a competition reaction, control reaction, or reaction mixture is about or more than about 5 ⁇ , 10 ⁇ , 30 ⁇ , 100 ⁇ , or 200 ⁇ . In some embodiments, the concentration of a competition probe in a competition reaction, control reaction, or reaction mixture is less than about 5 ⁇ , 10 ⁇ , 30 ⁇ , 100 ⁇ , or 200 ⁇ . In some embodiments, the concentration of a test compound in a competition reaction or reaction mixture is about or more than about 5 ⁇ , 10 ⁇ , 30 ⁇ , 100 ⁇ , or 200 ⁇ . In some embodiments, the concentration of a test compound in a competition reaction, control reaction, or reaction mixture is less than about 5 ⁇ , 10 ⁇ , 30 ⁇ , 100 ⁇ , or 200 ⁇ .
  • the competition probe, test compound, or both may be provided in excess quantities relative to the mutant Ras in a competition reaction, control reaction, or reaction mixture.
  • the mutant Ras may be provided in excess quantities relative to the competition probe, test compound, or both in a competition reaction, control reaction, or reaction mixture.
  • the ratio of competition probe and/or test compound to mutant Ras in a competition reaction, control reaction, or reaction mixture may be saturating.
  • the ratio of competition probe and/or test compound to mutant Ras in a competition reaction, control reaction, or reaction mixture may be non-saturating. The ratio can be calculated in terms of concentration, moles, or mass.
  • the ratio of competition probe and/or test compound to mutant Ras in a competition reaction, control reaction, or reaction mixture may be about or at least about 0.001; 0.002; 0.003; 0.004; 0.005; 0.006; 0.007; 0.008; 0.009; 0.01; 0.02; 0.03; 0.04; 0.05; 0.06; 0.07; 0.08; 0.09; 0.1; 0.2; 0.3; 0.4; 0.5; 0.6; 0.7; 0.8; 0.9; 1.0; 1.1; 1.2; 1.3; 1.4; 1.5; 1.6; 1.7; 1.8; 1.9; 2.0; 2.5; 3.0; 3.5; 4.0; 4.5; 5.0; 5.5; 6.0; 6.5; 7.0; 7.5; 8.0; 8.5; 9.0; 9.5; 10; 11; 12; 13; 14; 15; 16; 17; 18; 19; 20; 25; 30; 35; 40; 45; 50; 55; 60; 65; 70; 75; 80; 85; 90; 95; 100
  • the ratio of competition probe and/or test compound to mutant Ras in a competition reaction, control reaction, or reaction mixture may be up to about 0.001; 0.002; 0.003; 0.004; 0.005; 0.006; 0.007; 0.008; 0.009; 0.01; 0.02; 0.03; 0.04; 0.05; 0.06; 0.07; 0.08; 0.09; 0.1; 0.2; 0.3; 0.4; 0.5; 0.6; 0.7; 0.8; 0.9; 1.0; 1.1; 1.2; 1.3; 1.4; 1.5; 1.6; 1.7; 1.8; 1.9; 2.0; 2.5; 3.0; 3.5; 4.0; 4.5; 5.0; 5.5; 6.0; 6.5; 7.0; 7.5; 8.0; 8.5; 9.0; 9.5; 10; 11; 12; 13; 14; 15; 16; 17; 18; 19; 20; 25; 30; 35; 40; 45; 50; 55; 60; 65; 70; 75; 80; 85; 90; 95; 100; 200
  • the test compound may be provided in excess quantities relative to the competition probe in a competition reaction or reaction mixture, or vice versa.
  • the ratio of test compound to competition probe in a competition reaction or reaction mixture may be saturating.
  • the ratio of test compound to competition probe in a competition reaction or reaction mixture may be non- saturating. The ratio may be calculated in terms of concentration, moles, or mass.
  • the ratio of test compound to competition probe in a competition reaction or reaction mixture may be about or more than about 0.001; 0.002; 0.003; 0.004; 0.005; 0.006; 0.007; 0.008; 0.009; 0.01; 0.02; 0.03; 0.04; 0.05; 0.06; 0.07; 0.08; 0.09; 0.1; 0.2; 0.3; 0.4; 0.5; 0.6; 0.7; 0.8; 0.9; 1.0; 1.1; 1.2; 1.3; 1.4; 1.5; 1.6; 1.7; 1.8; 1.9; 2.0; 2.5; 3.0; 3.5; 4.0; 4.5; 5.0; 5.5; 6.0; 6.5; 7.0; 7.5; 8.0; 8.5; 9.0; 9.5; 10; 11; 12; 13; 14; 15; 16; 17; 18; 19; 20; 25; 30; 35; 40; 45; 50; 55; 60; 65; 70; 75; 80; 85; 90; 95; 100; 200; 300; 400; 500;
  • competition reaction or reaction mixture may be up to about 0.001; 0.002; 0.003; 0.004; 0.005; 0.006; 0.007; 0.008; 0.009; 0.01; 0.02; 0.03; 0.04; 0.05; 0.06; 0.07; 0.08; 0.09; 0.1; 0.2; 0.3; 0.4; 0.5; 0.6; 0.7; 0.8; 0.9; 1.0; 1.1; 1.2; 1.3; 1.4; 1.5; 1.6; 1.7; 1.8; 1.9; 2.0; 2.5; 3.0; 3.5; 4.0; 4.5; 5.0; 5.5; 6.0; 6.5; 7.0; 7.5; 8.0; 8.5; 9.0; 9.5; 10; 11; 12; 13; 14; 15; 16; 17; 18; 19; 20; 25; 30; 35; 40; 45; 50; 55; 60; 65; 70; 75; 80; 85; 90; 95; 100; 200; 300; 400; 500; 600; 700; 800; 900; or 1,000.
  • a competition reaction, control reaction, or reaction mixture may comprise one or more buffers, non-limiting examples of which include sodium carbonate buffer, sodium bicarbonate buffer, borate buffer, phosphate buffer, Tris buffer, MOPS buffer, HEPES buffer, and any combination thereof.
  • a buffer may optionally comprise sodium chloride, potassium chloride, one or more other salts, and any combination thereof.
  • a competition reaction, control reaction, or reaction mixture may be contained in any suitable reaction site.
  • the reaction site may be a container, such as a well of a multi-well plate, a plate, a tube, a chamber, a flow cell, a chamber or channel of a micro-fluidic device, or a chip.
  • the reaction site may be a partition within a solution, such as a droplet (e.g., within an emersion mixture).
  • the disclosed assay can be performed in an iterative manner.
  • an initial test compound with a desired binding property to any of the Ras proteins disclosed herein can be used as a competition probe in a subsequent round of screening assay.
  • the test compound can be first modified to incorporate a reactive moiety such that it covalently binds to a Ras mutant disclosed herein.
  • Such test compound can serve as a competition probe for screening for other candidates test compounds with, e.g., higher binding affinity to the Ras mutant protein as compared to the initial test compound.
  • This iterative process can allow successive screening for test compounds having improved proved properties including without limitation, higher binding affinity, higher selectivity against a particular Ras protein, or higher on or off rate of binding.
  • the disclosure provides a mutant Ras comprising a substituted amino acid.
  • the substituted amino acid is a reactive amino acid that permits covalent conjugation between the mutant Ras and a competition probe exhibiting the ability to react with the reactive amino acid; and
  • the substituted amino acid is not a cysteine or an aspartic acid at position 12 or 13 relative to SEQ ID NO: 1 when optimally aligned.
  • the reactive amino acid is cysteine, lysine, tyrosine, aspartic acid, glutamic acid, or a non-natural amino acid.
  • the reactive amino acid is cysteine.
  • the non-natural amino acid comprises a reactive moiety.
  • the competition probe competes for binding in the Switch II pocket of the mutant Ras.
  • the substituted amino acid is at a non-conserved position in Ras.
  • the substituted amino acid is at a position selected from position 62, 64, 65, 69, 74, 76, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 106, and any combination thereof relative to SEQ ID NO: 1 when optimally aligned, such as from position 62, 92, 95, and any combination thereof relative to SEQ ID NO: 1 when optimally aligned.
  • the substituted amino acid is a cysteine at position 62, 92, or 95 relative to SEQ ID NO: 1 when optimally aligned.
  • the substituted amino acid is a proteinogenic, natural, standard, non-standard, non-canonical, essential, non-essential, or non-natural amino acid.
  • the substituted amino acid has a positively charged side chain, a negatively charged side chain, a polar uncharged side chain, a non-polar side chain, a hydrophobic side chain, a hydrophilic side chain, an aliphatic side chain, an aromatic side chain, a cyclic side chain, an acyclic side chain, a basic side chain, or an acidic side chain.
  • the substituted amino acid has a nucleophilic or electrophilic side chain.
  • the substituted amino acid is a reactive amino acid that permits covalent conjugation between the mutant Ras and a competition probe exhibiting the ability to react with the reactive amino acid;
  • the substituted amino acid is a cysteine or an aspartic acid at position 12 or 13 relative to SEQ ID NO: 1 when optimally aligned; and
  • the mutant Ras is selected from the group consisting of mutant MRAS, mutant ERAS, mutant RRAS2, mutant RALA, mutant RALB, mutant RIT1, and any combination thereof.
  • the reactive amino acid is cysteine.
  • the competition probe is capable of binding the mutant Ras.
  • the competition probe competes for binding in the Switch II pocket of the mutant Ras.
  • the mutant Ras is selected from the group consisting of RALA, RALB, and any combination thereof.
  • a mutant Ras may comprise one or more additional mutations, including any one or more of the Ras mutations described herein.
  • one or more additional mutations in a mutant Ras may be at a position selected from position 12, 13, 14, 18, 19, 22, 59, 60, 61, 63, 117, 146, and any combination thereof relative to SEQ ID NO: 1 when optimally aligned, such as from position 12, 13, 18, 61, 146, and any
  • one or more additional mutations in a mutant Ras may be selected from G12A, G12C, G12D, G12F, G12L, G12R, G12S, G12V, G13A, G13C, G13D, G13R, G13S, G13V, V14G, V14I, A18D, A18T, L19F, Q22K, A59T, G60E, Q61E, Q61H, Q61K, Q61L, Q61P, Q61R, E63K, Kl 17N, A146P, A146T, A146V, and any combination thereof, such as from G12A, G12C, G12D, G12R, G12S, G12V, G13C, G13D, G13R, G13S, G13V, A18D, Q61H, Q61K, Q61L, Q61R, Kl 17N, A146T, and any combination thereof relative to SEQ ID NO: 1 when optimally aligned.
  • a mutant RAS is selected from a mutant KRAS, mutant HRAS, mutant NRAS, mutant RALA, mutant RALB, and any combination thereof. [148] In some embodiments, a mutant RAS is a mutant KRAS.
  • one or more additional mutations in a mutant KRAS may be selected from G12D, G12V, G13D, G12C, G12A, G12S, G12R, G13C, Q61H, A146T, Q61H, Q61L, Q61R, Q61H, G13S, G12G13R, G12F, Q61K, G13D, A146V, G13A, G13V, G12D, A146T, G13D, A59T, V14I, Q22K, G12F, K117N, Q61P, L19F, K117N, G12C, L19F, Q61E, G12L, G12V, G13G, Q61K, V14G, Q61L, A18D, G12G, E63K, A146P, A146V, G13G, GlO Al linsG, G12V, L19F, G13V, G12I, G60G, G12N, D173D,
  • a mutant RAS is a mutant HRAS.
  • one or more additional mutations in a mutant HRAS may be selected from G13R, G12V, Q61R, Q61L, Q61K, G12S, G12D, H27H, G12C, G13V, G13D, Q61G13S, Q61H, G12R, Q61R, G12A, G13C, Q61H, Y4H, E62G, Q61K, Y4fs*2, A59T, Q61P, Q61H, Q61L, V81M, K117N, K117N, A11 S, AHA, G13I, A18V, Q61R, Q61R, M72I, R123H, P179L, E3fs* 17, G10_Al linsG, G12N, G12_G13insAG, G12G12T, G13G, V14G, V14V, G15S, G15D, S
  • a mutant RAS is a mutant NRAS.
  • one or more additional mutations in a mutant NRAS is selected from Q61R, Q61K, G12D, G13D, Q61L, G12S, Q61R, G12C, G13R, Q61K, G12V, Q61H, G12A, G13V, Q61H, Q61H, Q61L, G13C, G12R, Q61P, G13A, G13S, A18T, Q61E, G60E, Q61Q, A59T, R68T, G12D, A146T, Q61R, G13G, E62Q, A59D, G13D, A11T, G10E, Q61L, Q61L, D92N, G12C, G75G, S65C, G12V, E62fs*6, T58T, Q61K, Q22K, D154G, G12N, Y64N, A146T, A59
  • a mutant RAS is a mutant MRAS.
  • one or more additional mutations in a mutant MRAS is selected from E154*, V94I, P120P, P151L, E47G, M1_A2>IS, VI 131, L133F, V6I, T137S, 1901, L16L, R138K, D165N, E143Q, A28T, R138S, I90M, Q140K, D129N, R173T, P120L, I136S, T54M, N149S, A145A, L171L, R112C, L29F, R138M, D195D, D129G, R78Q, A2V, R105H, D64D, G141R, D9N, S99S, V164V, and any combination thereof relative to SEQ ID NO: 5 when optimally aligned.
  • a mutant RAS is a mutant ERAS.
  • one or more additional mutations in a mutant ERAS is selected from F177F, R185W, A97T, G174R, S193S, G48S, D71N, P140S, G139V, L194L, V149M, VI 191, S181L, V52M, C226*, F120L, V188M, A97V, R103R, R31C, R32H, D69N, L117L, K6T, A165A, L61V, H70H, D69D, E24*, R103I, H171L, R27R, E24K, I129I, E41D, H227Q, A165S, I59S, and any combination thereof relative to SEQ ID NO: 6 when optimally aligned.
  • a mutant RAS is a mutant RRAS2.
  • one or more additional mutations in a mutant RRAS2 is selected from A70T, Q72L, V202A, V202V, Q72H, A167T, Q134Q, G24D, R147Q, S186fs*>16, D8N, Y82*, F204L, G24G, A29A, A158V, R117C, R63Q, Q72H, G24V, A158T, R63R, A167A, D44E, K53M, K177T, D49Y, K159Q, and any combination thereof relative to SEQ ID NO: 7 when optimally aligned.
  • a mutant RAS is a mutant RALA.
  • one or more additional mutations in a mutant RALA is selected from R176*, V20A, G23D, A158S, G23S, N81 S, D42N, G59W, V25E, G88W, II 81, F168C, N10K, E174*, R84*, E116D, K193*, R108M, D49G, Q63*, Q63H, L14F, Q63R, SHY, G21A, R176R, R198I, Q110H, K7E, Y82C, LI 12V, E141K, A177A, V154M, L32Q, 1641, Q63Q, E147*, G59R, R84Q, K134E, and any combination thereof relative to SEQ ID NO: 8 when optimally aligned.
  • a mutant RAS is a mutant RALB.
  • one or more additional mutations in a mutant RALB is selected from E106K, G23V, R144S, M19K, V125V, K129N, K194K, S85R, E141K, T69T, S94L, G24C, P122S, I18T, Q110H, S22S, K196N, LI 121, R79*, K197R, E60*, T31T, R84W, K200I, 111 IT, P45P, K180K, G71R, E175K, M19T, R135Q, S100S, F169L, R79Q, M19I, V125F, R52G, L124L, G23R, R136S, N188S, G23E, T161T, II UN, E106E, R162W, G23A, and any combination thereof relative to SEQ ID NO: 9 when optimally aligned.
  • a mutant RAS is a mutant RIT1.
  • one or more additional mutations in a mutant RIT1 is selected from M90I, F211L, A57G, D51V, R168H, D173N, R122*, R112C, M90I, A153V, R122L, R183H, K34T, F161fs*47, Q40L, A192T, G133E, V174V, L138L, L71V, R122Q, R45Q, A166delA, S19L, I73S, D216Y, E81Q, M90I, L74M, D56Y, K196fs* 12, SlOdelS, R86W, F82C, T38A, A77P, F41F, R63R, K23E, F108L, D172N, R120*, R212R, T124T, A77S, F82L, D87N, D172E, K34N, P199P, and
  • the disclosure provides a polynucleotide encoding any mutant Ras described herein.
  • the polynucleotide comprises DNA or RNA.
  • the polynucleotide encodes a mutant Ras selected from the group consisting of SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, and any combination thereof.
  • a polynucleotide described herein can be obtained using chemical synthesis, molecular cloning or recombinant methods, DNA or gene assembly methods, artificial gene synthesis, PCR, or any combination thereof. Methods of chemical polynucleotide synthesis are well known in the art and need not be described in detail herein. One of skill in the art can use the sequences provided herein and a commercial DNA synthesizer to produce a desired DNA sequence.
  • a polynucleotide comprising a desired sequence can be inserted into a suitable cloning or expression vector, and the cloning or expression vector in turn can be introduced into a suitable host cell for replication and amplification, as further discussed herein.
  • Polynucleotides may be inserted into host cells by any means known in the art. Cells may be transformed by introducing an exogenous polynucleotide, for example, by direct uptake, endocytosis, transfection, F-mating, chemical transformation, or electroporation.
  • the exogenous polynucleotide can be maintained within the cell as a non- integrated expression vector (such as a plasmid) or integrated into the host cell genome.
  • the polynucleotide so amplified can be isolated from the host cell by methods well known within the art. Alternatively, nucleic acid amplification methods (e.g., PCR) allow reproduction of DNA sequences.
  • RNA can be obtained by using the isolated DNA in an appropriate expression vector and inserting it into a suitable host cell. When the cell replicates and the DNA is transcribed into RNA, the RNA can then be isolated using methods well known to those of skill in the art. Alternatively, RNA can be obtained by transcribing the isolated DNA, for example, by an in vitro transcription reaction using an RNA polymerase. Alternatively, RNA can be obtained using chemical synthesis.
  • Suitable cloning vectors may be constructed according to standard techniques, or may be selected from a large number of cloning vectors available in the art. While the cloning vector selected may vary according to the host cell intended to be used, useful cloning vectors will generally have the ability to self-replicate, may possess a single target for a particular restriction endonuclease, and/or may carry genes for a marker that can be used in selecting clones containing the expression vector.
  • Suitable examples include plasmids and bacterial viruses, e.g., pUC18, pUC19, Bluescript (e.g., pBS SK+) and its derivatives, mpl8, mpl9, pBR322, pMB9, ColEl, pCRl, RP4, phage DNAs, and shuttle vectors such as pSA3 and pAT28.
  • Bluescript e.g., pBS SK+
  • mpl8 mpl9 mpl9
  • pBR322 mpl9
  • ColEl ColEl
  • pCRl pCRl
  • RP4 phage DNAs
  • shuttle vectors such as pSA3 and pAT28.
  • the disclosure provides an expression vector comprising any of the polynucleotides described herein.
  • a polynucleotide may be located in an expression vector.
  • An expression vector may be a construct, which is capable of delivering, and preferably expressing, one or more gene(s) or sequence(s) of interest in a host cell.
  • expression vectors include, but are not limited to, viral vectors (e.g., adenoviruses, adeno- associated viruses, and retroviruses), naked DNA or RNA expression vectors, plasmids, cosmids, phage vectors, DNA or RNA expression vectors associated with cationic condensing agents, DNA or RNA expression vectors encapsulated in liposomes, and certain eukaryotic cells, such as producer cells.
  • viral vectors e.g., adenoviruses, adeno- associated viruses, and retroviruses
  • naked DNA or RNA expression vectors e.g., plasmids, cosmids, phage vectors
  • DNA or RNA expression vectors associated with cationic condensing agents DNA or RNA expression vectors encapsulated in liposomes
  • certain eukaryotic cells such as producer cells.
  • An expression vector may allow easy and efficient replication, cloning, and/or selection.
  • an expression vector may additionally include nucleic acid sequences that permit it to replicate in the host cell, such as an origin of replication, one or more therapeutic genes and/or selectable marker genes and other genetic elements known in the art such as regulatory elements directing transcription, translation and/or secretion of the encoded protein.
  • Expression vector components may generally include, but are not limited to, one or more of the following: a signal sequence; an origin of replication; one or more marker genes; and suitable transcriptional controlling elements (such as promoters, enhancers and terminator).
  • suitable transcriptional controlling elements such as promoters, enhancers and terminator.
  • one or more translational controlling elements are also usually required, such as ribosome binding sites, translation initiation sites, internal ribosome entry site, and stop codons.
  • the expression vector may be used to transduce, transform or infect a cell, thereby causing the cell to express nucleic acids and/or proteins other than those native to the cell.
  • the expression vector optionally includes materials to aid in achieving entry of the nucleic acid into the cell, such as a viral particle, liposome, protein coating or the like.
  • suitable expression vectors are known in the art for protein expression, by standard molecular biology techniques. Such expression vectors are selected from among conventional vector types including insects, e.g., baculovirus expression, or yeast, fungal, bacterial or viral expression systems. Other appropriate expression vectors, of which numerous types are known in the art, can also be used for this purpose. Methods for obtaining cloning and expression vectors are well-known (see, e.g., Green and Sambrook, Molecular Cloning: A Laboratory Manual, 4th edition, Cold Spring Harbor Laboratory Press, New York (2012)).
  • the disclosure provides a host cell comprising any of the
  • the disclosure provides a host cell comprising any of the expression vectors described herein.
  • Any host cell capable of expressing heterologous DNA can be used for the purpose of isolating a Ras or mutant Ras protein or the polynucleotides encoding a Ras or mutant Ras protein.
  • Suitable host cells include, but are not limited to, mammalian (e.g., human, such as HEK or HeLa; mouse, such as a 3T3 or cells derived from Swiss, BALB/c or NIH mice; hamster, such as CHO; monkey, such as COS), bacterial (e.g., Escherichia coli, Bacillus subtilis, Pseudomonas,
  • Streptomyces e.g., Saccharomyces cerevisiae, Schizosaccharomyces pombe, Kluyveromyces lactis
  • insect e.g., Drosophila melanogaster, High Five, Spodoptera frugipedera Sf9 host cells.
  • the expression vectors containing the polynucleotides of interest can be introduced into a host cell by any of a number of appropriate means, including electroporation, chemical transformation, transfection employing calcium chloride, rubidium chloride, calcium phosphate, DEAE-dextran, or other substances; microprojectile
  • a mutant Ras is purified from a host cell.
  • a mutant Ras is produced using in vitro or cell-free protein synthesis, for example using a cell-free translation system comprising a cell extract such as Escherichia coli cell extract, rabbit reticulocyte cell extract, wheat germ cell extract, or insect cell extract.
  • the expressed protein may be recovered, isolated, and/or optionally purified from the cell, cell extract, or from the culture medium, by appropriate means known to one of skill in the art.
  • the proteins are isolated in soluble form following cell lysis, or extracted using known techniques, e.g., in guanidine chloride.
  • the proteins may be further purified using any of a variety of conventional methods including, but not limited to: liquid chromatography such as normal or reversed phase, using HPLC, FPLC and the like; affinity chromatography such as with inorganic ligands or monoclonal antibodies; size exclusion chromatography; immobilized metal chelate chromatography; gel electrophoresis; and the like.
  • liquid chromatography such as normal or reversed phase, using HPLC, FPLC and the like
  • affinity chromatography such as with inorganic ligands or monoclonal antibodies
  • size exclusion chromatography size exclusion chromatography
  • immobilized metal chelate chromatography immobilized metal chelate chromatography
  • gel electrophoresis gel electrophoresis
  • the disclosure provides a kit for performing any of the methods described herein.
  • the kit is for selecting a Ras antagonist.
  • the kit comprises a mutant Ras.
  • the mutant Ras is any of the mutant Ras proteins described herein.
  • the mutant Ras has a cysteine mutation at a position other than position 12 or 13 relative to SEQ ID NO: 1 when optimally aligned.
  • the kit comprises instructions for using the mutant Ras in a competition reaction between a competition probe and a test compound.
  • the kit further comprises the competition probe.
  • the kit further comprises one or more test compounds.
  • Kits can comprise one or more elements disclosed herein in relation to any of the various aspects, in any combination.
  • Reagents and other materials in a kit may be contained in any suitable container, and may be in an immediately usable form or require combination with other reagents in the kit or reagents supplied by a user (e.g., dilution of a concentrated composition or reconstitution of a lyophilized composition).
  • a kit may provide one or more buffers, non-limiting examples of which include sodium carbonate buffer, sodium bicarbonate buffer, borate buffer, phosphate buffer, Tris buffer, MOPS buffer, HEPES buffer, and any combination thereof.
  • a kit may comprise a control sample, e.g., for use as a positive control, negative control, or
  • the kit comprises instructions for use of the kit in accordance with one or more methods disclosed herein.
  • a method for using the kit comprises combining in a reaction mixture or a competition reaction a mutant Ras, a competition probe, and a test compound and detecting a decrease in binding between the mutant Ras and the competition probe as compared to binding of the mutant Ras in the absence of the test compound.
  • the disclosure provides a substrate having attached thereto a complex comprising a mutant Ras and a competition probe.
  • the mutant Ras can be any of the mutant Ras proteins described herein.
  • the mutant Ras comprises a substituted amino acid that is a reactive amino acid that permits covalent conjugation between the mutant Ras and the competition probe.
  • the substituted amino acid is not a cysteine or an aspartic acid at position 12 or 13 relative to SEQ ID NO: 1 when optimally aligned.
  • the competition probe is covalently bound to the mutant Ras at the reactive amino acid.
  • the reactive amino acid comprises a reactive moiety.
  • the competition probe binds in the Switch II pocket of the mutant Ras.
  • the substituted amino acid is at a non-conserved position in Ras.
  • the substituted amino acid is at position 62, 92, or 95 relative to SEQ ID NO: 1 when optimally aligned.
  • the substituted amino acid is a cysteine at position 62, 92, or 95 relative to SEQ ID NO: 1 when optimally aligned.
  • the mutant Ras may comprise one or more additional mutations.
  • the substrate can take any of a variety of forms.
  • the substrate is in a form selected from the group consisting of beads, microparticles, nanoparticles, nanocrystals, fibers, microfibers, nanofibers, nanowires, nanotubes, mats, planar sheets, planar wafers or slides, multi-well plates, optical slides, flow cells, channels, and any combination thereof.
  • a substrate may further include one or more additional structures, capillaries, wells, flow cells, channels (e.g., microfluidic channels), and the like.
  • suitable substrate materials are available.
  • substrate materials include, but are not limited to, inorganic materials such as silica based substrates (e.g., glass, quartz, fused silica, silicon, or the like), metals (e.g., gold), ceramics, or titanium dioxide; semiconductor materials; composite materials; organic materials such as polymer or plastic materials (e.g., poly(methyl methacrylate), polyethylene, polypropylene, polystyrene, cellulose, agarose, dextran, polyvinyl chloride, nylons, polyesters, polycarbonates, cyclic olefin polymers, natural polymer, synthetic polymer, or any of a variety of organic substrate materials conventionally used as supports for reactive media); and any combinations thereof.
  • inorganic materials such as silica based substrates (e.g., glass, quartz, fused silica, silicon, or the like), metals (e.g., gold), ceramics, or titanium dioxide
  • semiconductor materials e.g., silicon dioxide
  • composite materials organic materials such as polymer or plastic
  • the substrate comprises a material selected from the group consisting of glass, quartz, fused silica, silicon, metal, polymers, plastics, ceramics, composite materials, and any combination thereof.
  • molecules e.g., competition probe, a mutant Ras
  • the terms "immobilized” and “attached” are used interchangeably herein, and both terms are intended to encompass direct, indirect, covalent, or non-covalent attachment, unless indicated otherwise. In some embodiments, covalent attachment may be preferred.
  • the molecules e.g., competition probe, a mutant Ras
  • a substrate material comprises a material that is reactive, such that under specified conditions, a molecule (e.g., competition probe, a mutant Ras) can be attached directly to the surface of the substrate.
  • a substrate material comprises an inert substrate or matrix (e.g., glass slides, gold surface, polymer beads, or other substrate material) that has been "functionalized", for example by application of a layer or coating of an intermediate material comprising a reactive moiety which permit attachment (e.g., covalent attachment) to molecules, such as proteins or small molecules.
  • substrates include, but are not limited to, carboxymethylated dextran supported on an inert substrate such as gold.
  • the molecules e.g., competition probe, a mutant Ras
  • the intermediate material e.g., the dextran
  • the intermediate material may itself be non-covalently attached to the substrate or matrix (e.g., the gold substrate).
  • the complex is attached to the substrate by the mutant Ras. In some embodiments, the complex is attached to the substrate by the competition probe.
  • Attachment may be effected by means of a reactive moiety.
  • a molecule e.g., competition probe, a mutant Ras
  • a substrate to which molecules are attached comprises a reactive moiety.
  • the disclosure provides systems for performing any of the methods described herein.
  • the disclosure provides a system for selecting a Ras antagonist.
  • the system comprises a computer configured to receive a user request to perform a competition reaction.
  • the system comprises a reaction module that prepares the competition reaction, the competition reaction comprising a mutant Ras, a competition probe that is capable of binding the mutant Ras, and a test compound.
  • the system comprises a detection module that detects a decrease in binding between the mutant Ras and the competition probe as compared to binding of the mutant Ras in the absence of the test compound.
  • the mutant Ras is any of the mutant Ras proteins described herein.
  • the mutant Ras comprises a cysteine mutation that is not at position 12 or 13 relative to SEQ ID NO: 1 when optimally aligned.
  • the competition probe is capable of covalently modifying the mutant Ras at the cysteine mutation.
  • the test compound inhibits covalent modification of the mutant Ras by the competition probe.
  • one or more steps in sample processing, preparing the competition reaction, performing the competition reaction, detecting binding, and/or analysis are automated by the system.
  • automation may comprise the use of one or more liquid handlers and associated software.
  • liquid handlers from PerkinElmer, Caliper Life Sciences, Tecan, Eppendorf, Apricot Design, and Agilent Automation Solutions.
  • detecting comprises a real-time detection instrument.
  • the various steps may be implemented as various blocks, operations, tools, modules or techniques which, in turn, may be implemented in hardware, firmware, software, or any combination thereof.
  • some or all of the blocks, operations, techniques, etc. may be implemented in, for example, a custom integrated circuit (IC), an application specific integrated circuit (ASIC), a field programmable logic array (FPGA), a programmable logic array (PLA), etc.
  • the computer is configured to receive a user request to perform a competition reaction on a test compound.
  • the computer may receive the user request directly (e.g., by way of an input device such as a keyboard, mouse, or touch screen operated by the user) or indirectly (e.g., through a wired or wireless connection, including over the internet).
  • an input device such as a keyboard, mouse, or touch screen operated by the user
  • indirectly e.g., through a wired or wireless connection, including over the internet.
  • Non-limiting examples of users include an individual, medical personnel, clinicians, laboratory personnel, insurance company personnel, a health care provider, a health care manager, others in the health care industry, or electronic system (e.g., one or more computers, and/or one or more servers).
  • a computer can comprise one or more processors.
  • Processors may be associated with one or more controllers, calculation units, and/or other units of a computer system, or implanted in firmware as desired.
  • the routines may be stored in any computer readable memory such as in RAM, ROM, flash memory, a magnetic disk, a laser disk, or other storage medium.
  • this software may be delivered to a computing device via any known delivery method including, for example, over a communication channel such as a telephone line, the internet, a wireless connection, etc., or via a
  • transportable medium such as a computer readable disk, flash drive, etc.
  • the computer system may be understood as a logical apparatus that can read instructions from media (e.g., software) and/or network port (e.g., from the internet), which can optionally be connected to a server having fixed media.
  • a computer system may comprise one or more of a CPU, disk drives, input devices such as keyboard and/or mouse, and a display (e.g., a monitor).
  • Data communication such as transmission of instructions or reports, can be achieved through a communication medium to a server at a local or a remote location.
  • the communication medium can include any means of transmitting and/or receiving data.
  • the communication medium can be a network connection, a wireless connection, or an internet connection. Such a connection can provide for communication over the World wide Web.
  • a system can comprise one or more detection modules for performing one or more of mass spectrometry, enzyme-linked immunosorbent assay (ELISA), surface plasmon resonance, solid phase extraction, liquid chromatography, or any combination thereof.
  • the detection module may detect binding, covalent modification, mass- to-charge ratio, gas-phase ions, absorbance, fluorescence, luminescence, color, an
  • electrochemical signal current, or any combination thereof.
  • the system comprises a report generator that sends a report to a recipient.
  • the report contains results from the detection module.
  • the report generator identifies one or more test compounds as an inhibitor of Ras.
  • the report generator identifies one or more test compounds as not an inhibitor of Ras.
  • the report generator may send a report automatically in response to production of data (e.g., binding, fragmentation, or fluorescence intensity) by the system, such as in the form of data analysis performed by mass spectrometry or surface plasmon resonance analysis software. Alternatively, the report generator may send a report in response to instructions from a user.
  • Results of methods described herein will typically be assembled in a report.
  • a report may contain raw signal intensity data, processed signal intensity data (e.g., graphical displays, calculation of binding affinity), a conclusion that one or more test compounds is a Ras antagonist, a conclusion that one or more test compounds is not a Ras antagonist, and/or quantification of a concentration, binding affinity, or degree of covalent modification.
  • the report comprises test compounds identified as antagonists of Ras and excludes test compounds not identified as antagonists of Ras.
  • the report comprises test compounds identified as antagonists of Ras and test compounds not identified as antagonists of Ras.
  • the software routines used to generate the report can be run on a computer.
  • the report can be generated automatically upon receiving data.
  • the report can be generated in response to a user request.
  • the report may also be stored in any suitable medium, such as in RAM, ROM, flash memory, a magnetic disk, a laser disk, or other storage medium.
  • the report may be delivered to a computing device via any known delivery method including, for example, over a communication channel such as a telephone line, the internet, a wireless connection, etc., or via a transportable medium, such as a computer readable disk, flash drive, etc.
  • the report may be transmitted to a recipient at a local or remote location using any suitable communication medium.
  • the communication medium can be a network connection, a wireless connection, or an internet connection.
  • a report can be transmitted over such networks or connections (or any other suitable means for transmitting information, including but not limited to mailing a physical report, such as a print-out) for reception and/or for review by a recipient.
  • the recipient can be, but is not limited, to the user, an individual, medical personnel, clinicians, laboratory personnel, insurance company personnel, a health care provider, a health care manager, others in the health care industry, or electronic system (e.g., one or more computers, and/or one or more servers).
  • the report generator sends the report to a recipient's device, such as a personal computer, phone, tablet, or other device.
  • the report may be viewed online, saved on the recipient's device, or printed.
  • the disclosure provides a computer readable medium comprising codes that, upon execution by one or more processors, implements a method according to any of the methods disclosed herein. In some embodiments, execution of the computer readable medium implements a method of selecting a Ras antagonist.
  • execution of the computer readable medium implements a method of selecting a Ras antagonist, the method comprising: responsive to a user request to perform a competition reaction on a test compound, performing a competition reaction on the test compound in response to the user request, wherein the competition reaction comprises a mutant Ras, a competition probe that is capable of binding the mutant Ras, and a test compound; detecting a decrease in binding between the mutant Ras and the competition probe as compared to binding of the mutant Ras in the absence of the test compound; and generating a report that contains results for detection of a decrease in binding. Examples of competition probes, mutant Ras, and parameters for performing competition reactions are provided above.
  • the report generator identifies the test compound as an inhibitor of Ras.
  • Computer readable medium may take many forms, including but not limited to, a tangible storage medium, a carrier wave medium, or physical transmission medium.
  • Nonvolatile storage media include, for example, optical or magnetic disks, such as any of the storage devices in any computer(s) or the like, such as may be used to implement the calculation steps, processing steps, etc.
  • Volatile storage media include dynamic memory, such as main memory of a computer.
  • Tangible transmission media include coaxial cables; copper wire and fiber optics, including the wires that comprise a bus within a computer system.
  • Carrier-wave transmission media can take the form of electric or electromagnetic signals, or acoustic or light waves such as those generated during radio frequency (RF) and infrared (TR) data communications.
  • RF radio frequency
  • TR infrared
  • Common forms of computer readable media therefore include for example: a floppy disk, a flexible disk, hard disk, magnetic tape, any other magnetic medium, a CD-ROM, DVD or DVD-ROM, any other optical medium, punch cards paper tape, any other physical storage medium with patterns of holes, a RAM, a PROM and EPROM, a FLASH-EPROM, any other memory chip or cartridge, a carrier wave transporting data or instructions, cables or links transporting such a carrier wave, or any other medium from which a computer can read programming code and/or data. Many of these forms of computer readable media may be involved in carrying one or more sequences of one or more instructions to a processor for execution.
  • the pellet was resuspended in bacterial protein extraction reagent (B-Per, Fisher Scientific) containing protease inhibitor cocktail (Pierce Protease Inhibitor tablets, EDTA free).
  • the supernatant was incubated for 1 h with Co-affinity beads (Pierce HisPur resin, -2 mL bed volume per 1 L initial culture) at 4 °C.
  • the loaded beads were then washed with lysis buffer containing 2 mM BME, and the protein was eluted with buffer containing 250 mM imidazole.
  • Ni-agarose beads Qiagen
  • the partially purified protein was either fully labeled with the desired compound (incubation overnight with an excess of compound at room temperature and several hours at 37 °C (if necessary), labeling checked by mass-spectrometry analysis), frozen down and stored at -80 °C, or used for further purification.
  • the freshly prepared and purified protein was then concentrated to 5-20 mg/mL and used for the X-ray crystallography trays.
  • the described assays can be carried out with either the cleaved or uncleaved form of the protein.
  • KRAS mutant proteins were produced with one substituted amino acid selected from E62C, D92C, and H95C and with either glycine at the 12 position (WT) or an additional mutation to aspartic acid at the 12 position (G12D) relative to SEQ ID NO: 1 when optimally aligned. These mutations are depicted on an X-ray crystal structure in Fig. 2. These mutants were tested for reactivity (e.g., covalent modification of the KRAS mutant) with a panel of competition probes that bind the Switch II binding pocket and covalently modify the substituted amino acid with appropriately placed electrophiles based on modeling/docking studies.
  • RALA mutant proteins were produced with one mutation to cysteine at the 23 position (G23C) relative to SEQ ID NO: 8 when optimally aligned.
  • KRAS mutant proteins were produced with one mutation to cysteine at the 12 position (G12C) relative to SEQ ID NO: 1 when optimally aligned.
  • the RALA and KRAS mutants were tested for reactivity (e.g., covalent modification of the mutant) with a panel of competition probes that bind the Switch II binding pocket and covalently modify the substituted amino acid with appropriately placed electrophiles based on modeling/docking studies.
  • One such inhibitor covalently bound to RAS via G12 is depicted in Fig. 2. Screening was carried out by mass spectrometry on an Agilent RapidFire or ThermoScientific Q Exactive system.
  • Mutant Ras is incubated with competition probe under conditions suitable for binding.
  • concentrations of free mutant Ras and competition probe-bound mutant Ras are detected and quantified using mass spectrometry.
  • the binding interaction between an affinity-tagged competition probe and mutant Ras is measured, for example, by using an ELISA assay.
  • Example 5 Intact protein screening for inhibitors of mutant Ras under conditions where the mutant Ras protein is limiting ([Competition probe] » [mutant Ras])
  • the concentration of free competition probe is detected and quantified using mass
  • Mutant Ras is incubated with competition probe under conditions suitable for binding.
  • the Ras mutant is proteolytically digested.
  • the competition probe-induced decrease in unmodified mutant Ras is monitored by mass spectrometry.
  • Example 7 Triple-Quadrupole (QQQ) mass spectrometry protocol for K-Ras D92C binding using competition probe CP-008
  • Example 8 Fluorescence polarization assay for Ras binding using competition probe
  • a Ras competition probe is conjugated to a fluorophore at a suitable position that does not interfere with the probe's binding to Ras to produce a fluorescent competition probe (FL- CP).
  • a suitable fluorophore may comprise any of the various fluorescent probes disclosed herein .
  • GDP -loaded Ras is diluted in a suitable assay buffer.
  • a series of calibration fluorescence measurements are performed to determine: a) the background fluorescence intensity of the assay buffer; b) the fluorescence polarization of the FL-CP at assay concentration alone in the assay buffer; and c) the fluorescence polarization of the FL-CP at assay concentration added to the GDP-loaded Ras at assay concentration in assay buffer under conditions of maximal binding between the CP and Ras.
  • (a) represents background fluorescence
  • (b) represents 100% binding of a test compound
  • (c) represents 0% binding of a test compound.
  • test compounds are incubated in assay buffer along with Ras and FL-CP such that the FL-CP is limiting ([FL-CP] ⁇ [Ras]), the fluorescence polarization value is measured, and this value is compared to the fluorescence calibration values previously determined.
  • FL-CP FL-CP
  • RV-CP Ras-CP
  • Example 9 FRET quenching assay for Ras binding using competition probe
  • a Ras competition probe is conjugated to a FRET donor fluorophore at a suitable position that does not interfere with the probe's binding to Ras to produce a fluorescent competition probe (FL-CP).
  • Suitable fluorophores include any of the various fluorescent probes disclosed herein.
  • Ras protein is conjugated to an appropriate FRET acceptor fluorophore at a location within the FRET radius of the switch II binding pocket to create a fluorescent Ras-acceptor, loaded with GDP, and diluted in a suitable assay buffer.
  • a series of calibration fluorescence measurements are performed at approximately the wavelength of emission of the FL-CP fluorophore to determine: (a) the background fluorescence intensity of the assay buffer; (b) the fluorescence intensity of FL-CP at assay concentration alone in the assay buffer (unquenched); and (c) the fluorescence polarization of the FL-CP at assay concentration added to the GDP-loaded Ras-acceptor at assay
  • fluorescence measurement of (a) above represents background fluorescence
  • fluorescence measurement of (b) represents 100% binding of a test compound
  • fluorescence measurement of (c) represents 0% binding of a test compound.
  • test compounds are incubated in assay buffer in the presence of Ras-acceptor and FL-CP, the donor fluorescence is measured, and this value is compared to the fluorescence calibration values previously determined.
  • An alternative design utilizes a FRET pair to conduct the competition assay in which a competition probe conjugated to a FRET quencher (i.e., an acceptor in this alternative design) is brought to contact with a fluorescent Ras protein that is conjugated to an appropriate FRET donor.
  • a competition probe conjugated to a FRET quencher i.e., an acceptor in this alternative design
  • a series of calibration fluorescence measurements are performed at approximately the wavelength of emission of the Ras-donor to determine: (i) the background fluorescence intensity of the assay buffer; (ii) the fluorescence intensity of Ras- donor at assay concentration alone in the assay buffer (unquenched); and (iii) the fluorescence of the Ras-acceptor when FL-CP at assay concentration is added to the GDP-loaded Ras- donor at assay concentration in assay buffer under conditions of maximal binding between the FL-CP and Ras-acceptor, in which case the association of the FL-CP acceptor and Ras-donor quenches the donor fluorescence.
  • fluorescence measurement of (i) above represents background fluorescence
  • fluorescence measurement of (ii) represents 100% binding of a test compound
  • fluorescence measurement of (iii) represents 0% binding of a test compound.
  • test compounds are incubated in assay buffer in the presence of Ras-donor and FL-CP acceptor, the donor fluorescence is measured, and this value is compared to the fluorescence calibration values previously determined.
  • Example 10 ELISA assay for Ras binding using competition probe
  • a Ras competition probe is conjugated to a detectable ligand at a suitable position that does not interfere with the probe's binding to Ras to produce a ligand-conjugated competition probe (L-CP).
  • Suitable detectable ligands include any of those disclosed herein.
  • Hexahistidine-tagged Ras protein is loaded with GDP and diluted in a suitable assay buffer.
  • a test compound, hexahistidine-tagged Ras, and L-CP are added to the assay buffer.
  • the hexahistidine-tagged Ras is immobilized on a Ni-NTA coated substrate and washed with assay buffer to remove unbound compound.
  • an anti-ligand-HRP conjugate antibody is added to the hexahistidine-tagged Ras, the substrate is washed with assay buffer, TMB substrate is added, and absorbance of the solution is read at 650 nm.
  • the assay window is determined by a positive control (Hexahistidine-tagged Ras, no L-CP, assigned 100% inhibition) and a negative control (Hexahistidine-tagged Ras and L-CP at a time point where the covalent labeling has gone to completion, assigned 0% inhibition).
  • the assay can be performed to detect Ras rather than the competition probe.
  • the assay is started similarly by adding a test compound, hexahistidine-tagged Ras, and L-CP to the assay buffer. However, in this format the reaction is quenched by
  • the L-CP-Ras complex immobilizing the L-CP-Ras complex on a substrate coated with a receptor complementary to the ligand (in one embodiment, the ligand is biotin and the substrate is streptavidin-coated), and washing.
  • an anti-Ras or anti-polyhistidine HRP conjugate antibody is added, and an appropriate HRP substrate (e.g., TMB) is added followed by spectrophotometry at 650 nm.
  • the assay window is determined by a negative control (L-CP alone, no Ras, assigned 0% inhibition) and a positive control (L-CP and Ras at a time point when the covalent labeling has gone to completion, assigned 100% inhibition)

Abstract

L'invention concerne des compositions, des mélanges réactionnels, des protéines Ras mutantes, des kits, des substrats et des systèmes permettant de sélectionner un antagoniste de Ras, ainsi que des méthodes d'utilisation de ceux-ci.
PCT/US2016/057774 2015-10-19 2016-10-19 Méthode de criblage d'inhibiteurs de ras WO2017070256A2 (fr)

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US15/342,100 US9810690B2 (en) 2015-10-19 2016-11-02 Method for screening inhibitors of Ras
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JP2018533939A (ja) 2018-11-22
EP3364977A4 (fr) 2019-09-04
US9810690B2 (en) 2017-11-07
EP3364977A2 (fr) 2018-08-29

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